MBE Advance Access originally published online on May 2, 2008
Molecular Biology and Evolution 2008 25(8):1581-1592; doi:10.1093/molbev/msn105
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Articles |
Duplication and Functional Diversification of HAP3 Genes Leading to the Origin of the Seed-Developmental Regulatory Gene, LEAFY COTYLEDON1 (LEC1), in Nonseed Plant Genomes
* College of Life Sciences, Peking University, Beijing, China
Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
Centre for Evolutionary Biology and Institute of Biodiversity Science, Fudan University, Shanghai, China
E-mail: jiyang{at}fudan.edu.cn.
 |
Abstract |
|---|
 TOP Abstract IntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
The HAP3 gene encodes a subunit of the CCAAT-box-binding factor (CBF), a highly conserved trimeric activator that recognizes and binds the ubiquitous CCAAT promoter element with high affinity. Two types of HAP3 gene have been identified in plant genomes. The LEAFY COTYLEDON1 (LEC1)–type HAP3 genes encode a functionally specialized subunit of CBF, which is expressed specifically in developing seeds. In contrast, most non–LEC1-type HAP3 genes are expressed in various tissues. It has been proposed that the LEC1-type HAP3 genes originated from the duplication and functional divergence of non–LEC1-type HAP3 genes. However, it is not yet known when this duplication event took place or whether the LEC1-type HAP3 genes appeared at the same time as the origin of seed plants. Here we describe a comprehensive comparison of the duplication patterns of HAP3 genes in different plant genomes. We recognize a major expansion of the HAP3 gene family accompanying the origin and early diversification of land plants and postulate that retrotransposition and other mechanisms of gene duplication have been involved in the expansion of the plant HAP3 gene family. We provide evidence that the LEC1-type HAP3 genes originated in nonseed vascular plant genomes and demonstrate that they are inductively expressed under drought stress in nonseed plants. These genes, however, were recruited to a novel regulatory network in the early stages of seed plant evolution and steadily expressed during seed development and maturation.
Key Words: HAP3 gene family • lineage-specific duplication • LEC1 • gene origin
|
Introduction |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Gene duplication is a prevalent feature of plant genomes (Cronk 2001
) and can occur on 3 levels: genome duplication (polyploidization), segmental duplication, and single-gene duplication (Spring 2002; Cannon et al. 2004; Seoighe and Gehring 2004). The duplicates in a genome are hierarchically organized into families and superfamilies (Thornton and DeSalle 2000). Various potential evolutionary fates have been suggested for duplicate genes, including pseudogenization (nonfunctionalization), subfunctionalization, neofunctionalization, and retention of the original gene function (Ohno 1970; Lynch and Conery 2000; Zhang 2003). It has previously been shown that gene duplication followed by functional diversification has played an important role in providing novel genes that allow organisms to adapt to new environments (Ohno 1970; Chen et al. 2000; Hughes 2005).
The HAP3 gene encodes a subunit of the CCAAT-box-binding factor (CBF), a heterotrimeric complex composed of HAP2 (also known as CBF-B and NF-YA), HAP3 (CBF-A and NF-YB), and HAP5 (CBF-C and NF-YC). HAP3 interacts with HAP5 through histone fold motifs to form a tight dimer, which provides a complex surface for HAP2 association. The resulting trimer has a high affinity for DNA and functions as a major transcription factor recognizing CCAAT-box motifs (Mantovani 1999; Gusmaroli et al. 2001; Frontini et al. 2002; Romier et al. 2003). Each subunit of CBF contains a core region that is essential for subunit interactions and appears highly conserved throughout evolution.
The HAP3 subunit consists of 3 regions: an amino-terminal A domain, a central conserved B domain, and a carboxyl-terminal C domain (Li et al. 1992; Lotan et al. 1998). Based on sequence similarity of the conserved B domain, plant HAP3 subunits can be divided into 2 types: the LEAFY COTYLEDON1 (LEC1) type and the non–LEC1 type (Kwong et al. 2003; Lee et al. 2003). Functional analyses in Arabidopsis have revealed that the LEC1-type subunits represent a functionally specialized subunit of the CCAAT-binding transcription factor (Lee et al. 2003), which is expressed specifically in developing seeds, whereas most non–LEC1-type subunits are expressed in a variety of tissues (Zimmermann et al. 2004).
Seed formation is an intricate process that can be roughly divided into 2 distinct phases, an early morphogenesis phase and a late maturation phase (West and Harada 1993; Goldberg et al. 1994). During the early phase, the basic body plan of the embryonic plant is established, with the formation of various tissues and organ systems. Later, in the maturation phase, different gene expression programs result in the accumulation of storage compounds and acquisition of desiccation tolerance, finally leading to metabolic quiescence of embryos (Laux and Jürgens 1997; Harada 2001; Berleth and Chatfield 2002; Vicente-Carbajosa and Carbonero 2005). The LEC1 gene has been shown to function during both the early and the late stages of seed development (Harada 2001). Embryos of lec1 mutants have an abnormal morphology with highly vacuolated hypocotyls and rounded cotyledons. The lec1 cotyledons contain mature xylem elements and trichomes that are associated with true leaves and are not usually found in cotyledons. The lec1 mutant embryos exhibit no desiccation tolerance and accumulate no seed storage proteins (Meinke 1992; Meinke et al. 1994; West et al. 1994; Vicient et al. 2000). It has been proposed that LEC1 controls the accumulation of seed storage proteins through its regulation of FUSCA3 (FUS3) and ABSCISIC ACID INSENSITIVE 3 (ABI3), which encode key transcription factors controlling seed storage protein accumulation (Vicient et al. 2000; Kagaya et al. 2005; To et al. 2006). LEC1 is thus required for specification of cotyledon identity and specific aspects of seed maturation (Harada 2001; To et al. 2006). Recently, LEC1 was also found to be involved in GPA1-mediated abscisic acid (ABA) signaling transduction (Warpeha et al. 2007).
Multiple and distinct HAP3 genes have been identified in seed plant genomes (Li et al. 1992; Edwards et al. 1998; Miyoshi et al. 2003). Phylogenetic analysis suggests that the LEC1-type HAP3 genes from various flowering plants share a common origin, probably resulting from the duplication and functional divergence of the non–LEC1-type HAP3 genes (Kwong et al. 2003; Yazawa et al. 2004; Yang et al. 2005; Fambrini et al. 2006). However, the questions of when this duplication event took place and whether the LEC1-type HAP3 genes appeared at the same time as the origin of the seed plants remain unanswered. Furthermore, bryophytes, lycophytes, and ferns also go through an embryogenic process during their life cycles but do not make seed (Harada 2001; Gilbert 2006). They therefore require genetic factors regulating embryo development but not those involved in seed maturation. It is thus intriguing to investigate whether the LEC1-type HAP3 genes are present in these nonseed plant genomes.
The complete genome sequences now available allow detection of the evolutionary history of plant HAP3 genes by a genome-wide sequence comparison and phylogenomic analysis. Here we describe a comprehensive comparison of the duplication patterns of HAP3 genes in both seed plant and nonseed plant genomes and demonstrate that the duplicates which arose through different mechanisms diverged subsequently both in sequence and structure. We recognize a major expansion of the HAP3 gene family accompanying the origin and early diversification of land plants (embryophytes) and conclude that the LEC1-type HAP3 genes originated in the vascular plant genome prior to the divergence of seed plants, where expression analysis suggests that they play a role in desiccation tolerance.
|
Materials and Methods |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Phylogenomic Analysis
To explore the divergent pattern of HAP3 gene evolution and trace the origin of the LEC1-type HAP3 genes, we searched for the occurrence of HAP3 genes in various plant genomes, including 1 red alga (Cyanidioschyzon merolae), 2 green algae (Chlamydomonas reinhardtii and Volvox carteri), 1 moss (Physcomitrella patens), 1 lycophyte (Selaginella moellendorffii), and 2 seed plants (Arabidopsis thaliana and Oryza sativa). The whole-genome sequences of C. merolae, A. thaliana, and O. sativa are now available, but only unassembled whole-genome shotgun (WGS) sequences or scaffolds are available for C. reinhardtii, V. carteri, P. patens, and S. moellendorffii.
Coding sequences (CDSs) and complete gene sequences of C. merolae were downloaded from http://merolae.biol.s.u-tokyo.ac.jp/download/. Assembled scaffolds and annotated gene sequences (Assembly v.3.0) of C. reinhardtii were downloaded from http://genome.jgi-psf.org/Chlre3/Chlre3.download.ftp.html. The CDS and protein sequences of A. thaliana were downloaded from http://www.tigr.org. The CDS and protein sequences of annotated and predicted genes of O. sativa L. ssp. japonica were downloaded from http://www.tigr.org and http://rapdownload.lab.nig.ac.jp/. WGS sequences of V. carteri, P. patens, and S. moellendorffii were downloaded from ftp.ncbi.nih.gov.
Formatdb program implemented in stand-alone Blast 2.2.13 software (Altschul et al. 1997) was used to construct a Blast database for each genome. The TBlastN and BlastP programs were used to find sequences similar to HAP3 in each genome using the conserved B domain protein sequence of AtL1L (Kwong et al. 2003) as a query. For the 4 unassembled genomes, the CAP3 sequence assembly program (Huang and Madan 1999) was used to construct contigs from the WGS sequences obtained via blasting, with manual correction on some sites.
Multiple sequence alignments were performed using ClustalX (Thompson et al. 1997). Phylogenetic analyses of the HAP3 genes identified from P. patens, S. moellendorffii, A. thaliana, and O. sativa were conducted based on the conserved B domain of CDS sequences (fig. 1) and amino acid sequences (fig. 2). The HAP3 genes from C. reinhardtii (CrHAP3) and Mesostigma viride (MvHAP3) were used as alternative outgroups. The Neighbor-Joining (NJ) (Saitou and Nei 1987) method implemented in the MEGA4 program (Tamura et al. 2007) and the maximum likelihood (ML) (Felsenstein 1981) method implemented in PHYLIP 3.6 (Felsenstein 2005) were used to construct phylogenetic trees. NJ analyses for the nucleotide data set were performed using the JC69 (Jukes and Cantor 1969), Kimura 2-parameter (Kimura 1980), and maximum composite likelihood (Tamura et al. 2004) distance measures to examine their effects on topological stability, and the Poisson correction, Schwartz and Dayhoff (1979), and Jones-Taylor-Thorton (JTT) (Jones et al. 1992) models were used for the amino acid data set. ML analyses for the nucleotide data set were performed with DNAML (PHYLIP 3.6), assuming equal substitution rates among sites. ML trees for the amino acid data set were constructed using the JTT and Dayhoff PAM models with PROML (PHYLIP 3.6). The robustness of the tree topology was assessed by bootstrap analysis, with 1,000 resampling replicates for the NJ method and 100 replicates for the ML method.
|
|
Gene Structure Analysis
To determine the CDSs, each HAP3 gene identified in different plant genomes was used as a query to run BlastN against the expressed sequence tag (EST) and nonredundant nucleotide databases of National Center for Biotechnology Information to find related EST or messenger ribonucleic acid (mRNA) sequences. The GenScan program (http://genes.mit.edu/GENSCAN.html) was run to predict intron–exon structures for those HAP3 loci with no EST sequences in the database.
To confirm the predicted structures of P. patens and S. moellendorffii genes, we cloned the cDNA sequences using a standard 3' rapid amplification of cDNA ends (RACE) procedure (Sambrook and Russell 2001) with nested primers near the start codon (supplementary table 1a, Supplementary Material online). Total RNA was extracted using the RNAplant kit (TIANGEN BIOTECH CO LTD, Beijing, China). First-strand cDNA was produced using Promega M-MLV Reverse Transcriptase. Three cycles of polymerase chain reactions (PCRs) were performed using nested primers shown in supplementary table 1a (Supplementary Material online). Each reaction system (20 µl) contained 1x buffer with 2 mM MgCl2, 0.1 mM deoxynucleoside triphosphates (dNTPs), 1 µl of each primer, 1 unit of Taq DNA polymerase, and 1 µl single-stranded cDNA. Reactions were performed using the following conditions: initial denaturation at 94 °C for 5 min, followed by 30 cycles of 94 °C for 30 s, 58 °C for 1 min, 72 °C for 30 s, and a final extension at 72 °C for 5 min.
Amplification of LEC1 Homologues from Other Nonseed Plants
To detect the LEC1-type HAP3 genes that might be present in the bryophyte and pteridophyte genomes, a series of degenerate primers (supplementary table 1b, Supplementary Material online) were designed and used with various combinations to amplify the conserved B domain of potential LEC1-type HAP3 genes from 2 bryophyte species (Marchantia polymorpha and Tortula ruralis), 5 lycophyte species (Selaginella sinensis, Selaginella davidii, Isoetes sinensis, Isoetes yunguiensis, and Isoetes orientalis), and 1 fern species (Adiantum capillus-veneris). Species-specific primers were designed based on the central B domain of the LEC1-type HAP3 genes of each species with Tms above 65 °C. Thermal asymmetric interlaced (TAIL)-PCR was used to obtain the flanking A and C domains of the LEC1-like genes.
The genomic DNA of bryophytes was extracted from the gametophyte stage of the life cycle, whereas for lycophyte and fern species, the leaves of the sporophyte generation were used. DNA was extracted using a modified 2x Cetyl-Trimethyl-Ammonium-Bromide (CTAB) method (Doyle 1991). We used nested PCR to amplify the conserved B domain of potential LEC1-like genes. The first round of amplifications were performed in a reaction volume of 20 µl, containing 1x PCR buffer (10 mM Tris–HCl, pH 9.0, 50 mM KCl, 2.0 mM MgCl2, 0.1%Triton X-100), 100 µM of each dNTP, 20 ng of genomic DNA, 1 unit of Taq polymerase, and 2 µM outer primers. Reaction conditions were 94 °C for 5 min, 30 cycles of 94 °C for 30 s, 50 °C for 30 s, and 72 °C for 30 s and a final cycle of 72 °C for 5 min. The second round reactions were conducted under the same conditions except that 1 µl of 100-fold diluted first round product was used as template and a pair of inner primers were used for each reaction.
Arbitrary degenerate (AD) primers for TAIL-PCR were designed according to Liu and Whittier (1995) and Liu and Huang (1998). The primary reaction system of TAIL-PCR (20 µl) contained 1x PCR buffer, 2.0 mM MgCl2, 100 µM of each dNTP, about 20 ng of genomic DNA, 1 unit of Taq polymerase, 0.5 µM specific primer (SP1), and 2 µM AD primer. The secondary reaction (20 µl) contained 1x PCR buffer, 2.0 mM MgCl2, 100 µM of each dNTP, 1 µl of 100-fold diluted primary reaction product, 1 unit of Taq polymerase, 0.5 µM specific primer (SP2), and 2 µM of the same AD primers as the first round reaction. The tertiary reaction (20 µl) contained 1x PCR buffer, 2.0 mM MgCl2, 100 µM of each dNTP, 1 µl of 100-fold diluted secondary reaction product, 1 unit of Taq polymerase, 0.5 µM specific primer (SP3), and 2 µM of the same AD primers as the first round reaction. We used the TAIL-PCR procedure described by Liu and Huang (1998) with annealing reaction (65 °C and 44 °C) for 30 s and elongation reaction (72 °C) for 1 min. Ten microliters of secondary and tertiary products were run on 1.5% agarose gels for analysis.
PCR products were purified using the TIANGEN DNA Product Purification Mini Kit and cloned into the Promega pGEM-T vector and then sequenced in both directions using an ABI3730 automatic sequencer.
Complementation of the lec1-1 Mutant
To determine whether the LEC1-type HAP3 genes obtained from nonseed plant genomes possess LEC1 activity, we transferred the LEC1-type HAP3 gene from S. sinensis (SsLEC1) into the Arabidopsis lec1-1 mutant. Homozygous lec1-1 mutant plants were derived from heterozygous lec1-1 seeds provided by the Arabidopsis Biological Resource Center, and their genotypes were verified by PCR amplification. The pCAMBIA23XH binary T-DNA vector reconstructed from pCAMBIA2301 (CAMBIA, Canberra, Australia) was used as the transformation vector. It contains double cauliflower mosaic virus 35S promoters and a hygromycin resistance marker for the selection of transformed plants. A genomic fragment containing the putative open reading frame of SsLEC1 with additional NcoI and SpeI sites at either end was amplified using primers SsLEC1-NS and SsLEC1-SA (supplementary table 1c, Supplementary Material online). The amplified fragment was then inserted between the NcoI and SpeI sites of pCAMBIA23XH. Agrobacterium tumefaciens strain GV3101 containing the construct was used for vacuum infiltration of lec1-1 plants following the "in planta" transformation procedure of Bechtold et al. (1993). Seeds of transformed plants were germinated on MS medium containing 0.8% agar and 50 mg/l hygromycin to select transgenic plants.
Expression Pattern of the LEC1-Type HAP3 Genes in S. sinensis and A. capillus-veneris
Foliage leaves and strobili were used to examine whether the LEC1-type HAP3 gene from S. sinensis was expressed under normal growth conditions. Because S. sinensis is known as a resurrection plant, the foliage leaves of plants grown under dehydration stress conditions were also used for RNA extraction and reverse transcriptase–polymerase chain reaction (RT-PCR) analysis. Drought stress was imposed by withholding water. Foliage leaves under drought stress were collected every 24 h after stopping watering until the plant was totally desiccated. The desiccated plant was then rehydrated, and leaves were collected every 12 h until the plant recovered from desiccation.
The fern A. capillus-veneris, a lower plant model system for studying morphogenesis (Wada 2007), was also used in gene expression analysis because its free-living, autotrophic gametophyte facilitates the detection of LEC1 expression in the gametophyte stage. Drought treatment was also conducted on the sporophyte of A. capillus-veneris, with RNA extraction at 12-h intervals before rehydration and 6-h intervals after the rehydration and the plant being rehydrated before total desiccation because A. capillus-veneris is not a resurrection plant like S. sinensis.
Total RNA was extracted using TIANGEN RNAplant Total RNA Extraction kit and digested with Promega RQ1 RNase-free DNase to eliminate the remaining DNA. Promega M-MLV Reverse Transcriptase was used to produce first-strand cDNA. Nested PCRs were performed using primers designed based on the sequences of the SsLEC1 A domain (SsLEC1_f1 and SsLEC1_f2) and C domain (SsLEC1_r1 and SsLEC1_r2), respectively (supplementary table 1d, Supplementary Material online). The reaction system (20 µl) contained 1x buffer with 2 mM MgCl2, 0.1 mM dNTPs, 1 µl of each primer, 1 unit of Taq DNA polymerase, and 1 µl single-stranded cDNA. Reaction conditions were 94 °C for 5 min, 30 cycles of 94 °C for 30 s, 56 °C for 1 min, and 72 °C for 30 s and a final cycle of 72 °C for 5 min.
|
Results |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Phylogenomic and Gene Structural Analysis
A total of 10 HAP3-like genes were found in each of the A. thaliana and O. sativa genomes. Each species contains 2 LEC1-type and 8 non–LEC1-type HAP3 genes. Ten HAP3-like sequences were also found in the S. moellendorffii genome, which can be grouped into 5 pairs. The sequences in each pair showed a high level of similarity, including a pair of LEC1-type sequences. Selaginella moellendorffii is an outbred organism, and 2 haplotypes are represented in the WGS sequences (Wang et al. 2005
; http://selaginella.genomics.purdue.edu/data.html). Therefore, each pair probably represents 2 different alleles of a copy of the HAP3 gene. Six non–LEC1-type HAP3 genes were found in the P. patens genome. Each alga species, C. merolae, C. reinhardtii, and V. carteri possesses only a single copy of a non–LEC1-type HAP3 gene. The HAP3 nucleotide sequence data reported for P. patens, S. moellendorffii, C. merolae, C. reinhardtti, and V. carteri are available in the Third Party Annotation Section of the DDBJ/EMBL/GenBank databases under the accession numbers TPA: BK005956–BK005973. Gene loci, GenBank accession numbers, gene names, and related EST or mRNA sequences included in this paper are shown in supplementary table 2 (Supplementary Material online). We obtained 3 cDNA sequences for SmHAP3D2 and a single cDNA sequence for each of PpHAP3C, PpHAP3E, SmHAP3A2, SmHAP3B1, SmHAP3C1, and SmLEC1A2, using 3' RACE (GenBank accession numbers EU019897 [GenBank] –EU019906 [GenBank] ). No EST or cDNA sequence was found for Os1g0935100, PpHAP3D, SmLEC1A1, SmHAP3A1, SmHAP3C2, and SmHAP3D1. Comparison between EST, mRNA, and genomic DNA sequences revealed that At5g47670 (L1L), At2g38880, At2g37060, PpHAP3A, PpHAP3B, PpHAP3E, and SmHAP3D2 have more than one splice variant (fig. 1). The intron–exon structures of SmHAP3C1, SmHAP3D1, and PpHAP3E derived from 3'-RACE experiments are slightly different in the nonconservative C domain from those predicted.
Gene structural analysis revealed that plant HAP3 genes comprise 2 classes, intron-rich and intron-less/poor genes. CrHAP3, VcHAP3, PpHAP3E, PpHAP3F, SmHAP3D1, SmHAP3D2, At2G37060, At3g53340, At2G38880, Os05g0573500, Os05g0463800, and Os01g0834400 belong to the intron-rich class. These sequences have 2 introns in the B domain, with highly conserved intron positions and varied intron size. An extraordinarily small exon of only 6 nt was found at the 3' terminal of the B domain in most intron-rich genes. CmHAP3 also has 2 introns in the B domain, but the positions are completely different from those of other plants. Introns were also found in the A and C domains of intron-rich genes. However, the numbers and intron size are highly variable among species. The LEC1-type HAP3 genes (SmLEC1A1, SmLEC1A2, At1g21970, At5g47670, OsLEC1A, and OsLEC1B) and the rest of the non–LEC1-type HAP3 genes (PpHAP3A, PpHAP3B, PpHAP3C, PpHAP3D, SmHAP3A1, SmHAP3A2, SmHAP3B1, SmHAP3B2, SmHAP3C1, SmHAP3C2, At5g47640, At4g14540, At2g47810, At2g13570, At1g09030, Os01g0935100, Os01g0935200, Os08g0174500, Os07g0606600, and Os03g0413000) belong to the intron-less/poor class, containing no or only 1 intron, with the exceptions of PpHAP3A, PpHAP3B, and PpHAP3C, which have 2 or 3 introns, one located at the B domain and the others at the 5' untranslated regions (UTR) (fig. 1).
NJ and ML methods with different models of sequence evolution were used to infer the evolutionary relationships of different HAP3 genes. The phylogenetic trees reconstructed based on different models showed slight differences in topology from each other (supplementary figs. 1 and 4–6, Supplementary Material online). The tree topologies produced by the NJ and ML methods are similar in their overall structure but with minor differences in the within-clade relationships (supplementary figs. 2–6, Supplementary Material online). Alternate outgroup choices seem not to have any effect on tree topologies (see Supplementary Material online). Figure 1 shows the relationships of duplicate HAP3 genes derived from the NJ method with the Kimura 2-parameters model and their intron–exon structures in each land plant genome, with the HAP3 gene from C. reinhardtii (CrHAP3) used as outgroup. It is clear that intron-rich and intron-less/poor genes are separated into 2 lineages in all trees, even though only the section of sequence encoding the B domain was used in this analysis.
Figure 2 shows the phylogenetic relationships of all identified HAP3 genes from various plants, inferred by the NJ method based on amino acid sequences of the B domain of HAP3 proteins. It demonstrates that the intron-less/poor genes from various plants form a monophyletic group, suggesting a common origin of these genes (node A in fig. 2). The LEC1-type HAP3 genes, which appear to occur initially in the lycophyte genome, form a subsequent monophyletic lineage within this group (node B in fig. 2). The intron-rich non–LEC1-type HAP3 genes of land plants showed a closer relationship with the outgroup sequence, the algal HAP3, than did the intron-less/poor genes (fig. 2). The algal HAP3 gene also possesses multiple introns.
LEC1 Homologues Exist in Other Lycophyte and Fern Genomes
Phylogenomic analysis revealed the existence of LEC1-type HAP3 genes in the genome of S. moellendorffii. Our experimental results showed that the LEC1-type HAP3 genes are also present in other lycophyte and fern genomes, including those of S. sinensis, S. davidii, I. sinensis, I. yunguiensis, I. orientalis, and A. capillus-veneris (GenBank accession numbers: EF108291
[GenBank]
–EF108296
[GenBank]
). The deduced CDS lengths of these genes are 603, 528, 537, 537, 537, and 417 bp (partial), respectively. But we failed to detect any LEC1-type HAP3 genes in the genomes of the bryophytes M. polymorpha and T. ruralis.
The amino acid sequences of the B domain of the LEC1-type HAP3 genes obtained from lycophytes and ferns share 74–83% and 79–87% identity with Arabidopsis LEC1 and L1L, respectively. Sequence alignment revealed that the lycophyte and fern LEC1-type HAP3 genes possess most of the B domain amino acid residues that serve as signatures for the LEC1-type HAP3 genes (fig. 3).
|
SsLEC1 Can Complement the Arabidopsis lec1-1 Mutant
SsLEC1 from S. sinensis, driven by the cauliflower mosaic virus 35S promoter, was transferred into Arabidopsis plants homozygous for the lec1-1 mutation. About 3,000 T1 seeds were collected and dried. Seventeen of these seeds germinated on MS medium containing 50 mg/l hygromycin, and 10 of them successfully grew into seedlings in which expression of SsLEC1 was detected by RT-PCR. Unlike the lec1-1 mutant embryos, which have short axes and round trichome–bearing cotyledons, the embryos of the transgenic lec1-1 plants expressing SsLEC1 showed features similar to wild type, having normal axis length and curled trichome–free cotyledons (fig. 4). Kwong et al. (2003)
have previously shown that only the LEC1-like gene of Arabidopsis (L1L) can function in place of LEC1 when expressed ectopically but not the non–LEC1-type AHAP3 genes. Our results thus provide evidence that lycophyte LEC1-type HAP3 genes can play similar roles to seed plant LEC1-type HAP3 genes in regulating embryo development and maturation.
|
The LEC1-Type HAP3 Genes of S. sinensis and A. capillus-veneris Are Expressed under Drought Stress
RT-PCR analysis revealed that the LEC1-type HAP3 genes of S. sinensis and A. capillus-veneris are not expressed in plants grown under normal conditions, including the strobili of S. sinensis and the gametophyte of A. capillus-veneris. However, expression of SsLEC1 was detected in samples collected between the third and fifth day after stopping watering and reached a peak on the fifth day, then decreased dramatically (fig. 5A). The expression of SsLEC1 reoccurred at relatively low levels in samples collected between 12 and 60 h after rehydration (fig. 5A). AcLEC1 was also detected in samples collected at 60, 72, and 96 h after stopping watering and 12, 24, and 30 h after rehydration (fig. 5B).
|
|
Discussion |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Gene duplication is considered to be a major process in the generation of evolutionary novelty. Large-scale sequencing projects of different species have made it possible to explore whether certain gene duplication events have contributed to species divergence and the origins of species-specific features.
The data presented in this study provide strong evidence that successive rounds of gene duplication have taken place in the evolutionary history of the plant HAP3 gene family. The first round of duplication appears to have occurred accompanying the origin and early diversification of land plants because only one copy of the HAP3 gene was found in the genomes of C. reinhardtii and V. carteri, considered to be among the closest living relatives of the common ancestor of land plants (Karol et al. 2001). Because CBFs are transcription factors involved in many functions, the rapid expansion of the HAP3 gene family in land plant genomes might have contributed greatly to the morphological and functional innovations of land plant species. This scenario is consistent with the adaptive radiation model for the origin of new gene functions, which suggests that the evolution of new function may start with the amplification of an existing gene with some level of preadaption for that function, followed by a period of competitive evolution among the gene copies in response to specific selection pressures (Francino 2005).
Sequence comparison and gene structure analysis demonstrated that different mechanisms of gene duplication have been involved in the expansion of the plant HAP3 gene family. The intron-rich HAP3 genes of land plants show a high degree of similarity to those of green algae in sequence and structure, suggesting that they were descended directly from genes present in the algal ancestor of land plants. The intron-less/poor HAP3 genes show significant structural difference from the intron-rich genes and form a monophyletic group in the phylogenetic tree (fig. 2), indicating the existence of a common ancestor of these genes which occurred prior to the divergence of bryophytes and tracheophytes (vascular plants). It seems reasonable to postulate that the intron-less ancestral gene resulted from the retrotransposition of the intron-rich gene during evolution, with multiple introns being lost simultaneously. A newly formed retrogene has 3 hallmarks: lack of introns, containing a poly A tract, and remnants of flanking direct repeats (Brosius 1991; Emerson et al. 2004). These features, however, might be maintained only for a limited evolutionary time—introns can be inserted into intron-less genes and the poly A tracts and flanking repeats may be eroded within a relatively short time (Long 2001). The retrotransposition-mediated HAP3 duplicates have likely undergone such a process because no poly A tract or flanking repeats could be identified.
The second round of HAP3 gene duplications occurred in bryophyte and tracheophyte genomes independently. The intron-less ancestral gene experienced a lineage-specific process of intron insertion in bryophytes, predating subsequent rounds of duplication, which gave rise to the intron-poor genes of bryophytes, with an intron located at the same site in the B domain (fig. 1d). We compared the sequences of the newly inserted introns with those of intron-rich genes and blasted against the genome sequences but failed to find any sequence that showed significant similarity to the newly inserted introns, probably due to the high substitution rate of spliceosomal introns. Two hypotheses have been put forward to explain the origin of spliceosomal introns. The "intron-early" hypothesis postulates that introns appeared early in the evolution of life and were subsequently lost in most prokaryotes (Doolittle 1978; Gilbert 1987; Gilbert et al. 1997), whereas the "intron-late" hypothesis suggests that introns have been inserted into eukaryotic genes later in evolution (Cavalier-Smith 1985; Palmer and Logsdon 1991). Genome-wide analyses, however, have revealed extensive loss and gain of introns during the course of eukaryotic diversification (Rogozin et al. 2003; Zhaxybayeva and Gogarten 2003; Roy and Penny 2007). Frequent intron gain and loss have also been found in recently duplicated genes (Gotoh 1998; Knowles and McLysaght 2006), which supports the mixed model of intron evolution: a synthetic theory of intron-early and intron-late speculations. The pattern of intron evolution in HAP3 genes seems in agreement with the mixed model.
The intron-less ancestral gene in tracheophyte genomes did not undergo the intron-gain process but was duplicated several times with one copy diverging subsequently to become the ancestor of the LEC1-type HAP3 genes, before the divergence of lycophytes/ferns and seed plants (fig. 2). It has been proposed that the CBF complex containing the LEC1-type subunit is unlikely to serve a general role in transcription by optimizing promoter efficiency through its binding with CCAAT DNA sequences, as the CBF trimer containing the non–LEC1-type subunit does but rather to regulate embryonic processes by activating the transcription of specific genes that are required for embryo development in seed plants (Lotan et al. 1998). The lec1 mutant embryos not only exhibit abnormal morphological characteristics but also fail to accumulate seed-specific storage products, making them intolerant of full desiccation (Meinke et al. 1994). The potential function of SsLEC1 in regulating seed development and maturation was confirmed by complementation analysis of the A. thaliana lec1 mutant, which showed that SsLEC1 was able to complement all the defects of the lec1 mutant. It is thus reasonable to conclude that some gene copies had experienced a process of neofunctionalization following the duplication of the intron-less ancestral gene in tracheophyte genomes, leading to asymmetric evolution among duplicated genes (Yang et al. 2005).
We have shown, however, that the LEC1-type HAP3 genes occurred initially in nonseed plant genomes. The role of the LEC1-type HAP3 gene in regulating seed development is thus clearly a derived function evolved with the origin of seed plants. What role might the LEC1-type HAP3 gene play in nonseed species? RT-PCR analysis showed that SsLEC1 and AcLEC1 were not expressed under normal growing conditions but expression occurred during both dehydration and rehydration. This result suggests that the lycophyte and fern LEC1-type HAP3 genes are probably involved in protection from desiccation, a similar process to that found during the maturation phase of seed development. Warpeha et al. (2007) recently found that the LEC1 gene is involved in the GPA1-mediated ABA signal transduction pathway. This finding might provide clues as to how the LEC1-type HAP3 gene has facilitated the drought stress response in both vascular nonseed plants and the more derived seed plants because it is well documented that ABA plays important roles in regulating gene expression and signal transduction when plants are subjected to drought stress (Meurs et al. 1992; Xu and Bewley 1995; Shinozaki K and Shinozaki KY 1997; Bartels and Salamini 2001; Zhu 2002).
The role of the LEC1-type HAP3 gene in regulation of the vegetative desiccation tolerance in nonseed plants seems to be co-opted to the seed desiccation protection mechanism in the early stages of seed plant evolution by incorporating the LEC1-type HAP3 gene into a novel network regulating seed development and maturation. Gene co-option is known to play a major role in the evolution of development (True and Carroll 2002). Seed formation has long been regarded as one of the most striking innovations in the evolutionary history of land plants. Although the full regulatory network remains uncharacterized, there is strong evidence that the LEC1-type HAP3 gene is a central regulator of seed development (Lotan et al. 1998; Harada 2001; Kwong et al. 2003; Lee et al. 2003). It is interesting to note that the LEC1-type HAP3 gene is not only required for specific aspects of seed maturation but also plays a role in the specification of embryonic organ identity, including suspensor cell and cotyledon identities (Harada 2001). This probably suggests that functional shift has been involved in the process of co-option, resulting in a gene with different functions (multifunctionality). It has been proposed that multifunctionality is quite common among developmental regulatory genes, which seem to accrue new regulatory functions by changes in their expression pattern and, hence, their connections to upstream or downstream genes (Duboule and Wilkins 1998; Ganfornina and Sanchez 1999; True and Carroll 2002). Little is known currently about the mechanisms by which co-option of gene function takes place. However, it might be helpful to note that the CBF subunits can function not only by complex formation but also by individual interaction with other proteins (Chen et al. 2007). Wenkel et al. (2006) reported that CONSTANS (CO), which promotes Arabidopsis flowering, might replace AtHAP2 in the CBF complex and interact with AtHAP3 and AtHAP5 to form a heterotrimeric CO/AtHAP3/AtHAP5, playing an important role in the photoperiodic flowering pathway. The CCT domain of CO is highly similar to that of HAP2 in terms of structure (Wenkel et al. 2006). Warpeha et al. (2007) also showed that the LEC1-type subunit can physically interact with PRN1, an iron-containing member of the cupin superfamily, in the GPA1-mediated ABA signal transduction pathway.
The increasing number of sequenced genomes has intensified research into lineage-specific gene duplication events, as well as their roles in driving evolutionary novelty. Although more data are needed to decipher the evolutionary history of the plant HAP3 gene family, preliminary analyses of the available sequences demonstrate that plant HAP3 genes duplicated and evolved in different patterns associated with the origin and further diversification of land plants. The LEC1-type HAP3 gene, known to be essential for embryo development and seed formation, originated in nonseed lycophyte genomes but is absent from the genomes of bryophytes, which also undergo embryonic development in their life cycles. This suggests that duplicated HAP3 genes are involved in the genetic mechanisms behind the diversification of plant body plans. Phenotypically important changes can emerge along a specific lineage via changes in gene expression, in coding sequence evolution, or through other mechanisms (Liberles 2005). Detailed molecular characterization of duplicate HAP3 genes, particularly the temporal and spatial expression patterns of LEC1-type HAP3 genes in different phylogenetic groups, will offer new insights into how the duplicated HAP3 genes survived and acquired novel functions during evolution and what roles various HAP3 genes played in the evolution of important land plant adaptive traits.
|
Supplementary Material |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Supplementary figures 1–6 and tables 1 and 2 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).
|
Acknowledgements |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
We thank Dr Neelima Sinha and 2 anonymous reviewers for critical reading of the manuscript and valuable comments. This work was supported by the National Key Basic Research Program (973) (2007CB411607, 2003CB715904), National Natural Science Foundation of China (30370092), and Shanghai Leading Academic Discipline Project (B111).
|
Footnotes |
|---|
Neelima Sinha, Associate Editor
|
References |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res (1997) 25(17):3389–3402.
Bartels D, Salamini F. Desiccation tolerance in the resurrection plant Craterostigma plantagineum: a contribution to the study of drought tolerance at the molecular level. Plant Physiol (2001) 127:1346–1353.
Bechtold N, Ellis J, Pelletier G. In planta Agrobacterium mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. C R Acad Sci Paris Life Sci (1993) 316:1194–1199.
Berleth T, Chatfield S. Embryogenesis: pattern formation from a single cell. In: The Arabidopsis book—Somerville CR, Meyerowitz EM, eds. (2002) Rockville (MD): American Society of Plant Biologists. [cited 2008 May 30]. Available from: http://www.aspb.org/publications/arabidopsis/.
Brosius J. Retroposons-seeds of evolution. Science (1991) 251:753.
Cannon SB, Mitra A, Baumgarten A, Young ND, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol (2004) 4(1):10.[CrossRef][Medline]
Cavalier-Smith T. Selfish DNA and the origin of introns. Nature (1985) 315:283–284.[Medline]
Chen K, Durand D, Farach-Colton M. Notung: a program for dating gene duplications and optimizing gene family trees. J Comput Biol (2000) 7:429–447.[CrossRef][Web of Science][Medline]
Chen NZ, Zhang XQ, Wei PC, Chen QJ, Ren F, Chen J, Wang XC. AtHAP3b plays a crucial role in the regulation of flowering time in Arabidopsis during osmotic stress. J Biochem Mol Biol (2007) 40(6):1083–1089.[Web of Science][Medline]
Cronk QCB. Plant evolution and development in a post-genomic context. Nat Rev Genet (2001) 2:607–619.[CrossRef][Web of Science][Medline]
Doolittle WF. Genes in pieces: where they ever together? Nature (1978) 272:581–582.[CrossRef]
Doyle JJ. DNA protocols for plants-CTAB total DNA isolation. In: Molecular techniques in taxonomy—Hewitt GM, Johnston A, eds. (1991) Berlin (Germany): Springer. 283–293.
Duboule D, Wilkins AS. The evolution of ‘bricolage’ Trends Genet (1998) 14:54–59.
Edwards D, Murray JAH, Smith AG. Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiol (1998) 117:1015–1022.
Emerson JJ, Kaessmann H, Betrán E, Long M. Extensive gene traffic on the mammalian X chromosome. Science (2004) 303:537–540.
Fambrini M, Durante C, Cionini G, Geri C, Giorgetti L, Michelotti V, Salvini M, Pugliesi C. Characterization of LEAFY COTYLEDON1-LIKE gene in Helianthus annuus and its relationship with zygotic and somatic embryogenesis. Dev Genes Evol (2006) 216:253–264.[CrossRef][Web of Science][Medline]
Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 17:368–376.[CrossRef][Web of Science][Medline]
Felsenstein J. PHYLIP (phylogeny inference package). Version 3.6. In: Distributed by the author (2005) Seattle (WA): Department of Genome Sciences, University of Washington.
Francino MP. An adaptive radiation model for the origin of new gene functions. Nat Genet (2005) 37:573–578.[CrossRef][Web of Science][Medline]
Frontini M, Imbriano C, diSilvio A, Bell B, Bogni A, Romier C, Moras D, Tora L, Davidson I, Mantovani R. NF-Y recruitment of TFIID, multiple interactions with histone fold TAFIIs. J Biol Chem (2002) 277:5841–5848.
Ganfornina MD, Sanchez D. Generation of evolutionary novelty by functional shift. Bioessays (1999) 21:432–439.[CrossRef][Web of Science][Medline]
Gilbert SF. Developmental biology. (2006) 8th ed. Sunderland (MA): Sinauer Associates. [cited 2008 May 10]. Available from: http://8e.devbio.com/index.php.
Gilbert W. The exon theory of genes. Cold Spring Harb Symp Quant Biol (1987) 52:901–905.
Gilbert W, De Souza SJ, Long M. Origin of genes. Proc Natl Acad Sci USA (1997) 94:7698–7703.
Goldberg RB, de Paiva G, Yadegari R. Plant embryogenesis: zygote to seed. Science (1994) 266:605–614.
Gotoh O. Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes. Mol Biol Evol (1998) 15:1447–1459.
Gusmaroli G, Tonelli C, Mantovani R. Regulation of the CCAAT-binding NF-Y subunits in Arabidopsis thaliana. Gene (2001) 264:173–185.[CrossRef][Web of Science][Medline]
Harada JJ. Role of Arabidopsis LEAFY COTYLEDON genes in seed development. J Plant Physiol (2001) 158:405–409.[CrossRef][Web of Science]
Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res (1999) 9:868–877.
Hughes AL. Gene duplication and the origin of novel proteins. Proc Natl Acad Sci USA (2005) 102:8791–8792.
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci (1992) 8:275–282.
Jukes TH, Cantor CR. Evolution of protein molecules. In: Mammalian protein metabolism—Munro HN, ed. (1969) New York: Academic Press. 21–132.
Kagaya Y, Toyoshima R, Okuda R, Usui H, Yamamoto A, Hattori T. LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3. Plant Cell Physiol (2005) 46(3):399–406.
Karol KG, McCourt RM, Cimino MT, Delwiche CF. The closest living relatives of land plants. Science (2001) 294(14):2351–2353.
Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol (1980) 16:111–120.[CrossRef][Web of Science][Medline]
Knowles DG, McLysaght A. High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. Mol Biol Evol (2006) 23:1548–1557.
Kwong RW, Bui AQ, Lee H, Kong LW, Fischer RL, Goldberg RB, Harada JJ. LEAFY COTYLEDON1-LIKE defines a class of regulators essential for embryo development. Plant Cell (2003) 15:5–18.
Laux T, Jürgens G. Embryogenesis: a new start in life. Plant Cell (1997) 9:989–1000.[CrossRef][Web of Science][Medline]
Lee H, Fischer RL, Goldberg RB, Harada JJ. Arabidopsis LEAFY COTYLEDON1 represents a functionally specialized subunit of the CCAAT binding transcription factor. Proc Natl Acad Sci USA (2003) 100(4):2152–2156.
Li XY, Mantovani R, Hooft van Huijsduijnen R, Andre I, Beoist C, Mathis D. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res (1992) 20:1087–1091.
Liberles DA. Datasets for evolutionary comparative genomics. Genome Biol (2005) 6:117.[CrossRef][Medline]
Liu YG, Whittier RF. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics (1995) 25:674–681.[CrossRef][Web of Science][Medline]
Liu YG, Huang N. Efficient amplification of insert end sequences from bacterial artificial chromosome clones by thermal asymmetric interlaced PCR. Plant Mol Biol Rep (1998) 16:175–181.[CrossRef][Web of Science]
Long M. Evolution of novel genes. Curr Opin Genet Dev (2001) 11:673–680.[CrossRef][Web of Science][Medline]
Lotan T, Ohto M, Yee MK, West MAL, Lo R, Kwong RW, Yamagishi K, Fischer RL, Goldberg RB, Harada JJ. Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell (1998) 93:1195–1205.[CrossRef][Web of Science][Medline]
Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science (2000) 290:1151–1155.
Mantovani R. The molecular biology of the CCAAT-binding factor NF-Y. Gene (1999) 239:15–27.[CrossRef][Web of Science][Medline]
Meinke DW. A homoeotic mutant of Arabidopsis thaliana with leafy cotyledons. Science (1992) 258:1647–1650.
Meinke DW, Franzmann LH, Nickle TC, Yeung EC. Leafy cotyledon mutants of Arabidopsis. Plant Cell (1994) 6:1049–1064.[Abstract]
Meurs C, Basra AS, Karssen CM, van Loon LC. Role of abscisic acid in the induction of desiccation tolerance in developing seeds of Arabidopsis thaliana. Plant Physiol (1992) 98(4):1484–1493.
Miyoshi K, Ito Y, Serizawa A, Kurata N. OsHAP3 genes regulate chloroplast biogenesis in rice. Plant J (2003) 36:532–540.[CrossRef][Web of Science][Medline]
Ohno S. Evolution by gene duplication (1970) New York: Springer.
Palmer JD, Logsdon JM Jr. The recent origins of introns. Curr Opin Genet Dev (1991) 1:470–477.[CrossRef][Medline]
Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol (2003) 13:1512–1517.[CrossRef][Web of Science][Medline]
Romier C, Cocchiarella F, Mantovani R, Moras D. The NF-YB/NF-YC structure gives insight into DNA binding and transcription regulation by CCAAT factor NF-Y. J Biol Chem (2003) 278:1336–1345.
Roy SW, Penny D. Patterns of intron loss and gain in plants: intro loss-dominated evolution and a genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol (2007) 24(1):171–181.
Saitou N, Nei M. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 4:406–425.[Abstract]
Sambrook J, Russell DW. Molecular cloning: a laboratory manual (2001) 3rd ed. New York: Cold Spring Harbor Laboratory Press.
Schwartz R, Dayhoff M. Matrices for detecting distant relationships. In: Atlas of protein sequences and Structure. Washington (DC): Nat Biomed Res Found. 5(Suppl 3):353–358—Dayhoff M, ed. (1979).
Seoighe C, Gehring C. Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet (2004) 20(10):461–464.[CrossRef][Web of Science][Medline]
Shinozaki K, Shinozaki KY. Gene expression and signal transduction in water stress response. Plant Physiol (1997) 115:327–334.[CrossRef][Web of Science][Medline]
Spring J. Genome duplication strikes back. Nat Genet (2002) 31:128–129.[Web of Science][Medline]
Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the Neighbor-Joining method. Proc Natl Acad Sci USA (2004) 101:11030–11035.
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 24:1596–1599.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res (1997) 25(24):4876–4882.
Thornton JW, DeSalle R. Gene family evolution and homology: genomics meets phylogenetics. Annu Rev Genomics Hum Genet (2000) 1:41–73.[CrossRef][Web of Science][Medline]
To A, Valon C, Savino G, Guilleminot J, Devic M, Giraudat J, Parcy F. A network of local and redundant gene regulation governs Arabidopsis seed maturation. Plant Cell (2006) 18(7):1642–1651.
True JR, Carroll SB. Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol (2002) 18:53–80.[CrossRef][Web of Science][Medline]
Vicente-Carbajosa J, Carbonero P. Seed maturation: developing an intrusive phase to accomplish a quiescent state. Int J Dev Biol (2005) 49:645–651.[CrossRef][Web of Science][Medline]
Vicient CM, Bies-Etheve N, Delseny M. Changes in gene expression in the leafy cotyledon1 (lec1) and fusca3 (fus3) mutants of Arabidopsis thaliana L. J Exp Bot (2000) 51:995–1003.
Wada M. The fern as a model system to study photomorphogenesis. J Plant Res (2007) 120:3–16.[CrossRef][Web of Science][Medline]
Wang W, Tanurdzic M, Luo M, Sisneros N, Kim HR, Weng JK, Kudrna D, Mueller C, Arumuganathan K, Carlson J, et al, (16 co-authors). Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics. BMC Plant Biol (2005) 5:10–16.[CrossRef][Medline]
Warpeha KM, Upadhyay S, Yeh J, Adamiak J, Hawkins SI, Lapik YR, Anderson MB, Kaufman LS. The GCR1, GPA1, PRN1, NF-Y signal chain mediates both blue light and abscisic acid responses in Arabidopsis. Plant Physiol (2007) 143(4):1590–1600.
Wenkel S, Turck F, Singer K, Gissot L, Gourrierec J, Samach A, Couplanda G. CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell (2006) 18:2971–2984.
West MAL, Harada JJ. Embryogenesis in higher plants: an overview. Plant Cell (1993) 5:1361–1369.
West MAL, Yee KM, Danao J, Zimmerman JL, Fischer RL, Goldberg RB, Harada JJ. LEAFY COTYLEDONl is an essential regulator of late embryogenesis and cotyledon identity in Arabidopsis. Plant Cell (1994) 6:1731–1745.
Xu N, Bewley JD. The role of abscisic acid in germination, storage protein synthesis and desiccation tolerance in alfalfa (Medicago sativa L.) seeds, as shown by inhibition of its synthesis by fluridone during development. J Exp Bot (1995) 46:687–694.
Yang J, Xie Z, Glover BJ. Asymmetric evolution of duplicate genes encoding the CCAAT-binding factor NF-Y in plant genomes. New Phytol (2005) 165(2):623–632.[CrossRef][Web of Science][Medline]
Yazawa K, Takahata K, Kamada H. Isolation of the gene encoding carrot leafy cotyledon1 and expression analysis during somatic and zygotic embryogenesis. Plant Physiol Biochem (2004) 42:215–223.[CrossRef][Web of Science][Medline]
Zhang J. Evolution by gene duplication: an update. Trends Ecol Evol (2003) 18(6):292–298.[CrossRef]
Zhaxybayeva O, Gogarten JP. Spliceosomal introns: new insights into their evolution. Curr Biol (2003) 13(19):R764–R766.[CrossRef][Medline]
Zhu JK. Salt and drought stress signal transduction in plants. Annu Rev Plant Biol (2002) 53:247–273.[CrossRef][Medline]
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol (2004) 136:2621–2632.
CiteULike 
Connotea 
Del.icio.us What's this?
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||