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Patterns of Gene Duplication and Their Contribution to Expansion of Gene Families in Grapevine

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Abstract

Grapevine is an important fruit crop that has undergone a long history of evolution. Analysis of the whole genome sequence of grapevine has revealed presence of an early palaeo-hexaploid along with three complements. Thus, gene duplication and genome expansion are common in this genome. In this study, we identified 17,922 duplicated genes in the whole grapevine genome. Among these, 2,039; 628; 1,428; 722; and 2,942 were identified respectively as produced by genome-wide, tandem, proximal, retrotransposed, and DNA-based transposed duplications. Analyses of the evolutionary patterns for different types of duplication using non-synonymous and synonymous substitution rates uncovered a series of underlying rules. Thereafter, all the grapevine genes were classified into families, and the contributions of different types of duplication to the expansion of large families were revealed. No duplication type was solely responsible for the formation of any large gene family, but some families showed enrichment of a special type of duplication. On the basis of this study, we believe that uncovering the underlying rules for gene duplications, expansions of gene families, and their evolutionary styles will contribute significantly to a comprehensive understanding of the features of the grapevine genome.

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Acknowledgments

Financial support for this work was provided by the National Natural Science Foundation of China (NSFC accession No.: 31171931) and the National Natural Science Foundation of Hubei Province (No.: 2011CDB409).

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Authors and Affiliations

  1. Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China

    Nian Wang, Yue Xiang, Linchuan Fang, Haiping Xin & Shaohua Li

  2. Graduate School of Chinese Academy of Sciences, Beijing, 100049, China

    Yue Xiang, Linchuan Fang & Yajie Wang

  3. Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China

    Yajie Wang

  4. Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China

    Nian Wang & Shaohua Li

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  1. Nian Wang
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  2. Yue Xiang
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  3. Linchuan Fang
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  4. Yajie Wang
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  5. Haiping Xin
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Correspondence to Nian Wang or Shaohua Li.

Electronic Supplementary Material

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Supplementary Table 1

Duplication types for all grapevine genes. The names of genes are given according to the 12− V. vinifera genomic sequence (PDF 198 kb)

Supplementary Table 2

Valid pairs for genome-wide duplicated genes (PDF 37 kb)

Supplementary Table 3

Valid pairs for tandem duplicated genes (PDF 16 kb)

Supplementary Table 4

Valid pairs for proximal duplicated genes (PDF 29 kb)

Supplementary Table 5

Valid pairs for retrotansposed duplicated genes (PDF 18 kb)

Supplementary Table 6

Valid pairs for DNA-based transposed duplicated genes (PDF 58 kb)

Supplementary Table 7

Grapevine gene families. The information was summarized from plant gene family database (http://green.dna.affrc.go.jp/PGF-DB/index.html) (PDF 662 kb)

Supplementary Table 8

Expansion of grapevine gene families (PDF 16 kb)

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Wang, N., Xiang, Y., Fang, L. et al. Patterns of Gene Duplication and Their Contribution to Expansion of Gene Families in Grapevine. Plant Mol Biol Rep 31, 852–861 (2013). https://doi.org/10.1007/s11105-013-0556-5

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