PTGBase: an integrated database to study tandem duplicated genes in plants.

Jingyin Yu,Sadia Tehrim,Fengming Sun,Boshou Liao,Tao Ke,Wei Hua

doi:10.1093/database/bav017

Jingyin Yu, Sadia Tehrim + Show 4 more

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https://doi.org/10.1093/database/bav017

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Abstract

Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available.Database URL: http://ocri-genomics.org/PTGBase/.

Highlights

Angiosperms are an excellent example of a group of plants that provide a sound base for understanding gene duplication (GD) in higher eukaryotes
About 43, 47 and 56% of nucleotide binding site (NBS)-encoding disease resistance (R) genes in B. oleracea, B. rapa and Arabidopsis thaliana, respectively, were generated through tandem GD events; this shows that the rate of tandem duplicated genes is higher in Arabidopsis thaliana than in Brassica species
PTGBase is the first plant tandem duplicated genes database that embraces a wide spectrum of genome resources for genome-sequenced plant species

Summary

Introduction

Angiosperms are an excellent example of a group of plants that provide a sound base for understanding gene duplication (GD) in higher eukaryotes. All angiosperms underwent polyploidization events, and the fraction of recently duplicated genes is higher in plants than in other eukaryotes [4]. These genes originate as a result of at least six different modes of duplication including whole genome, tandem, proximal, DNAbased transposition, retrotransposition and dispersed duplications [5]. Tandem duplication events occur more frequently than other duplication modes and produce greater gene copy number and allelic variation. Tandem GDs have played roles in the evolution of different traits in various plant families like disease resistance in Solanaceae and Brassicaceae [9, 10], signal transduction in legumes [11], glucosinolate biosynthesis diversification in the mustard family [12], and defense response and secondary metabolism like indole alkaloid biosynthesis and tropane, piperidine and pyridine alkaloid biosynthesis in Brassica oleracea and Brassica rapa [13]

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