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Molecular Biology Reports

, Volume 39, Issue 5, pp 6267–6282 | Cite as

Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species

  • Yijun Wang
  • Dexiang Deng
  • Rong Zhang
  • Suxin Wang
  • Yunlong Bian
  • Zhitong Yin
Article

Abstract

B3 domain-containing proteins constitute a large transcription factor superfamily. The plant-specific B3 superfamily consists of four family members, i.e., LAV (LEC2 [LEAFY COTYLEDON 2]/ABI3 [ABSCISIC ACID INSENSITIVE 3] − VAL [VP1/ABI3-LIKE]), RAV (RELATED to ABI3/VP1), ARF (AUXIN RESPONSE FACTOR) and REM (REPRODUCTIVE MERISTEM) families. The B3 superfamily plays a central role in plant life, from embryogenesis to seed maturation and dormancy. In previous research, we have characterized ARF family, member of the B3 superfamily in silico (Wang et al., Mol Biol Rep, 2011, doi: 10.1007/s11033-011-0991-z). In this study, we systematically analyzed the diversity, phylogeny and evolution of B3 domain-containing proteins based on genomic resources of 11 sequenced species. A total of 865 B3 domain-containing genes were identified from 11 sequenced species through an iterative strategy. The number of B3 domain-containing genes varies not only between species but between gene families. B3 domain-containing genes are unevenly distributed in chromosomes and tend to cluster in the genome. Numerous combinations of B3 domains and their partner domains contribute to the sequences and structural diversification of the B3 superfamiy. Phylogenetic results showed that moss VAL proteins are related to LEC2/ABI3 instead of VAL proteins from higher plants. Lineage-specific expansion of ARF and REM proteins was observed. The REM family is the most diversified member among the B3 superfamily and experiences a rapid divergence during selective sweep. Based on structural and phylogenetic analysis results, two possible evolutional modes of the B3 superfamily were presented. Results presented here provide a resource for further characterization of the B3 superfamily.

Keywords

B3 domain-containing protein Diversity Phylogeny Evolution 

Notes

Acknowledgments

We are grateful to editors and reviewers for their helpful comments. This work is supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions, the Innovative Foundation of Yangzhou University (2011CXJ046, 2010CXJ035) and the Nature Science Foundation of Universities in Jiangsu Province (No. 09KJB180010).

Supplementary material

11033_2012_1448_MOESM1_ESM.tif (76 kb)
Supplementary Fig. 1 Strategy for identification of B3 genes. An iterative strategy was employed to isolate and validate B3 genes in this study. The core of this technique lies in the iteration of data mining and HMM profiles construction. Details of this method were described in the text (TIFF 75 kb)
11033_2012_1448_MOESM2_ESM.tif (143 kb)
Supplementary Fig. 2 Schematic organization of B3 proteins. Possible DNA-binding domains B3, zf-CW and AP2 are marked in glaucous, purple and golden, respectively. Other characterized regions auxin response factor domain Auxin_resp and heterodimerization domain AUX_IAA are colored in kelly and nattierblue, respectively. Accession numbers of representative genes are showed below single lines (TIFF 143 kb)
11033_2012_1448_MOESM3_ESM.tif (634 kb)
Supplementary Fig. 3 Phylogeny and residues constitution of consensus sequences from B3 domains. a Phylogenesis of consensus sequences of B3 domains. Symbols LEC2/ABI3, VAL, RAV and ARF represent consensus sequences of B3 domains from LEC2/ABI3, VAL, RAV and ARF proteins, respectively. REM-1B3, REM-2B3 and REM-3B3 denote consensus sequences from the first, second and third B3 domains of REM proteins, respectively. Signs 1wid and 1yel figure consensus sequences of B3 domains from Arabidopsis RAV1 and At1g16640 proteins, respectively. Nine consensus sequences of B3 domains are classified into four groups. b Multiple alignment of consensus sequences of B3 domains. Consensus sequences are generated from B3 domains of RAV1, At1g16640, 38 LEC2/ABI3, 32 VAL, 115 RAV, 279 ARF, 401 REM-1B3, 178 REM-2B3 and 45 REM-3B3, respectively. Characterized regions β sheets and α helixes are showed above. Residues in RAV1 which contact with DNA directly are emphasized by arrows (TIFF 633 kb)
11033_2012_1448_MOESM4_ESM.tif (139 kb)
Supplementary Fig. 4 Phylogenesis and gene structure of proliferated ARF genes. The left is the phylogenetic tree of proliferated ARF proteins. The right is schematic structures of proliferated ARF genes. Exons and introns are showed by filled boxes and single lines, respectively. Domains B3, ARF and Aux/IAA are marked in red, blue and yellow, respectively (TIFF 139 kb)
11033_2012_1448_MOESM5_ESM.tif (111 kb)
Supplementary Fig. 5 Phylogenesis of the REM family based on whole sequences. REM proteins are primarily divided into monocot-specific, eudicot-specific and mixed groups. Divergent subgroups are in groups. The eudicot-specific proliferation of REM genes was observed (emphasized as rosids REM genes expansion group in figure) (TIFF 110 kb)
11033_2012_1448_MOESM6_ESM.tif (140 kb)
Supplementary Fig. 6 Ka/Ks ratios of sister pairs of B3 genes containing two B3 domains. The sliding window analysis method was used to estimate selective pressures on B3 genes. The first and second B3 domains are displayed by red and green boxes, respectively (TIFF 139 kb)
11033_2012_1448_MOESM7_ESM.xls (234 kb)
Supplementary Table 1 B3 genes in 11 species. Details of 865 B3 genes, including locus name, gene nomenclature, chromosomal location, deduced protein length, the number, position and E-value of B3 domains are presented (XLS 234 kb)
11033_2012_1448_MOESM8_ESM.doc (45 kb)
Supplementary Table 2 B3 genes cluster. B3 genes, especially REM genes tend to cluster in genomic regions of higher plants. The largest cluster of B3 genes is in a 140 kb genomic region on sorghum chromosome 1 which contains 12 REM genes (DOC 45 kb)
11033_2012_1448_MOESM9_ESM.doc (28 kb)
Supplementary Table 3 Duplication dates of sister pairs of B3 genes. Duplication time of sister pairs was approximately estimated by calculating the d S value in this study (DOC 28 kb)

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Yijun Wang
    • 1
  • Dexiang Deng
    • 1
  • Rong Zhang
    • 1
  • Suxin Wang
    • 1
  • Yunlong Bian
    • 1
  • Zhitong Yin
    • 1
  1. 1.Key Laboratory of Jiangsu Province for Crop Genetics and Physiology, Key Laboratory of Ministry of Education for Plant Functional GenomicsYangzhou UniversityYangzhouChina

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