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

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.

Genomic Identification and Comparative Expansion Analysis of the Non-Specific Lipid Transfer Protein Gene Family in Gossypium

“…In addition, G. arboreum lost all the Type III and Type IX nsLTPs (Fig. S2), suggesting that the evolution of plants not only involves gene retentions, but also is accompanied by gene losses and mutations428. Meanwhile, the proportion of nsLTPs in each subfamily indicated that Type I seemed to have contracted while Type VIII expanded in G. hirsutum compared with its diploid progenitors (Fig.…”

“…These peptides are structurally characterized by an eight cysteine motif (8 CM) backbone with the general form C-Xn-C-Xn-CC-CXC-Xn-C-Xn-C, and the cysteine residues are linked by four disulfide bonds to stabilize a tertiary structure of a hydrophobic cavity23. Moreover, almost all nsLTPs carry an N-terminal secretory signal peptide (21–27 amino acids in length) in their nascent polypeptides, indicating that they are secreted proteins24. In previous studies, plant nsLTPs have been identified to participate in a range of biological processes, including cuticular wax and cutin synthesis, biotic and abiotic stress resistance, plant signaling, seed maturation and sexual reproduction24.…”

“…Moreover, almost all nsLTPs carry an N-terminal secretory signal peptide (21–27 amino acids in length) in their nascent polypeptides, indicating that they are secreted proteins24. In previous studies, plant nsLTPs have been identified to participate in a range of biological processes, including cuticular wax and cutin synthesis, biotic and abiotic stress resistance, plant signaling, seed maturation and sexual reproduction24. In some cases, nsLTPs are considered pathogenesis-related (PR) proteins and constitute the PR-14 family5.…”

“…The system categorized 267 nsLTPs into nine types (Type I-IX) based on a genome-wide analysis of rice ( Oryza sativa ), wheat ( Triticum aestivum ) and Arabidopsis thaliana . Then, nsLTPs in other plant species were also grouped according to Boutrot’s method with slight modifications49101112, and novel types such as Type X9 and Type XI4 were identified.…”

Genome-Wide Survey of Flavonoid Biosynthesis Genes and Gene Expression Analysis between Black- and Yellow-Seeded Brassica napus

“…Genome-wide analyses of gene superfamilies have been widely performed after the completion of numerous plant genome projects. For instance, numerous genome-wide studies of gene superfamilies have been performed in the diploid species, B. rapa and B. oleracea (Song et al, 2013; Duan et al, 2014; Li et al, 2014; Diehn et al, 2015; Lu et al, 2015). Several gene superfamilies have also been reported in the allotetraploid species B. napus (Sun et al, 2014; Raboanatahiry et al, 2015) However, a comprehensive analysis of the superfamily of genes underlying the flavonoid biosynthesis pathway in Brassica has not been reported to date.…”