Genome-Wide Survey and Expression Analysis of the Putative Non-Specific Lipid Transfer Proteins in Brassica rapa L

Jun Li,Guixin Yan,Kun Xu,Jiangwei Qiao,Xiaoming Wu,Tianyao Zhang,Guizhen Gao,Biyun Chen,Feng Li,Tianzhen Zhang

doi:10.1371/journal.pone.0084556

Abstract

BackgroundPlant non-specific lipid transfer proteins (nsLtps) are small, basic proteins encoded by multigene families and have reported functions in many physiological processes such as mediating phospholipid transfer, defense reactions against phytopathogens, the adaptation of plants to various environmental conditions, and sexual reproduction. To date, no genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. Therefore, as the first step and as a helpful strategy to elucidate the functions of BrnsLtps, a genome-wide study for this gene family is necessary.Methodology/Principal FindingIn this study, a total of 63 putative BrnsLtp genes were identified through a comprehensive in silico analysis of the whole genome of B. rapa. Based on the sequence similarities, these BrnsLtps was grouped into nine types (I, II, III, IV, V, VI, VIII, IX, and XI). There is no type VII nsLtps in B. rapa, and a new type, XI nsLtps, was identified in B. rapa. Furthermore, nine type II AtLtps have no homologous genes in B. rapa. Gene duplication analysis demonstrated that the conserved collinear block of each BrnsLtp is highly identical to those in Arabidopsis and that both segmental duplications and tandem duplications seem to play equal roles in the diversification of this gene family. Expression analysis indicated that 29 out of the 63 BrnsLtps showed specific expression patterns. After careful comparison and analysis, we hypothesize that some of the type I BrnsLtps may function like Arabidopsis pathogenesis-related-14 (PR-14) proteins to protect the plant from phytopathogen attack. Eleven BrnsLtps with inflorescence-specific expression may play important roles in sexual reproduction. Additionally, BrnsLtpI.3 may have functions similar to Arabidopsis LTP1.Conclusions/SignificanceThe genome-wide identification, bioinformatic analysis and expression analysis of BrnsLtp genes should facilitate research of this gene family and polyploidy evolution and provide new insight towards elucidating their biological functions in plants.

Highlights

Lipids are important chemicals involved in many aspects of development and growth in plants
A search for misannotated putative non-specific lipid transfer proteins (nsLtps) genes was conducted by local BlastP searches on the all proteins of B. rapa using the previously used 49 Arabidopsis nsLtps as query sequences [17] (Fig. 1)
We identified a total of 63 Brassica rapa nsLtp (BrnsLtp) in the whole genome of B. rapa (Table 1, Table S1, Table S2)

Summary

Introduction

Lipids are important chemicals involved in many aspects of development and growth in plants. The most common examples are the surface layers, cutin and suberin These structures are made up of hydrophobic polyesters of fatty acid derivatives and are known to be associated with biotic and abiotic stress. The lipids deposited in storage organs, such as seeds and fruits, are a crucial energy source for the growing populations of the world. Lipids and their derivatives play roles in many important cell-signaling pathways [1]. No genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. As the first step and as a helpful strategy to elucidate the functions of BrnsLtps, a genome-wide study for this gene family is necessary

Methods

Results

Conclusion