AUTHOR=Han Tianyu , Dong Heng , Cui Jie , Li Ming , Lin Sue , Cao Jiashu , Huang Li 

TITLE=Genomic, Molecular Evolution, and Expression Analysis of Genes Encoding Putative Classical AGPs, Lysine-Rich AGPs, and AG Peptides in Brassica rapa

JOURNAL=Frontiers in Plant Science

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.00397

DOI=10.3389/fpls.2017.00397

ISSN=1664-462X

ABSTRACT=<p>Arabinogalactan proteins (AGPs) belong to a class of Pro/Hyp-rich glycoproteins and are some of the most complex types of macromolecules found in plants. In the economically important plant species, <italic>Brassica rapa</italic>, only chimeric AGPs have been identified to date. This has significantly limited our understanding of the functional roles of AGPs in this plant. In this study, 64 <italic>AGPs</italic> were identified in the genome of <italic>B. rapa</italic>, including 33 classical AGPs, 28 AG peptides and three lys-rich AGPs. Syntenic gene analysis between <italic>B. rapa</italic> and <italic>A. thaliana</italic> suggested that the whole genome triplication event dominated the expansion of the <italic>AGP</italic> gene family in <italic>B. rapa</italic>. This resulted in a high retained proportion of the <italic>AGP</italic> family in the <italic>B. rapa</italic> genome, especially in the least fractionated subgenome. Phylogenetic and motif analysis classified the classical AGPs into six clades and three orphan genes, and the AG peptides into three clades and five orphan genes. Classical AGPs has a faster rate of molecular evolution than AG peptides revealed by estimation of molecular evolution rates. However, no significant differences were observed between classical AGPs and lys-rich AGPs. Under control conditions and in response to phytohormones treatment, a complete expression profiling experiment has identified five anther-specific <italic>AGPs</italic> and quite a number of <italic>AGPs</italic> responding to abscisic acid, methyl jasmonate and/or gibberellin. In this study, we presented a bioinformatics approach to identify important types of <italic>AGPs</italic>. Moreover, the association between their function and their protein structure, as well as the evolution and the expression of <italic>AGP</italic> genes were investigated, which might provide fundamental information for revealing the roles of AGPs in <italic>B. rapa</italic>.</p>