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

Abstract

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, Brassica rapa, 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 AGPs were identified in the genome of B. rapa, including 33 classical AGPs, 28 AG peptides and three lys-rich AGPs. Syntenic gene analysis between B. rapa and A. thaliana suggested that the whole genome triplication event dominated the expansion of the AGP gene family in B. rapa. This resulted in a high retained proportion of the AGP family in the B. rapa 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 AGPs and quite a number of AGPs responding to abscisic acid, methyl jasmonate and/or gibberellin. In this study, we presented a bioinformatics approach to identify important types of AGPs. Moreover, the association between their function and their protein structure, as well as the evolution and the expression of AGP genes were investigated, which might provide fundamental information for revealing the roles of AGPs in B. rapa.

Pectin De-methylesterification and AGP Increase Promote Cell Wall Remodeling and Are Required During Somatic Embryogenesis of Quercus suber

“…There is very scarce information about AGP sequences in the cork oak database, but there were some reports that related the selected AGPs to embryo formation, which suggested that they could also be expressed in somatic embryogenesis. Expression of AGP17, AGP18 , and AGP16 has been reported in siliques, containing embryos (Han et al, 2017); furthermore, AGP18 has been described as essential in female gametophyte formation (Acosta-García and Vielle-Calzada, 2004).…”

“…Increasing evidence has shown that AGPs have a role in reproductive tissues and in embryo development (Zhong et al, 2011; Geshi et al, 2013). In Arabidopsis , 85 AGPs have been identified (Showalter et al, 2010), however, there is little information on AGP genes in non-model species due to the heterogeneous and complex structure of these macromolecules (Pereira et al, 2016; Han et al, 2017). The analyses reported here have revealed the up-regulation of three different AGP genes, QsLys-rich-AGP17 , QsLys-rich-AGP18 , and QsAGP16L1 , and a progressive increase in AGP level of accumulation, by precipitation with β-Gluc-Yariv, from early to advanced stages of somatic embryogenesis.…”

Genome-Wide Identification, Molecular Evolution, and Expression Profiling Analysis of Pectin Methylesterase Inhibitor Genes in Brassica campestris ssp. chinensis

“…Seventeen loci of AtPMEIs did not have the orthologous gene in B. campestris . To know whether these loci were lost in B. campestris or were newly acquired in Arabidopsis , the analysis of their orthologous genes in other Brassicaceae species was performed on the basis of a previous study [ 34 ]. The results showed that 6 loci of AtPMEIs might be lost in B. campestris and 11 loci might arise after the divergence between Arabidopsis and B. campestris ( Table S3 ) .…”

The distinct functions of two classical arabinogalactan proteins BcMF8 and BcMF18 during pollen wall development in Brassica campestris

“…A recent study reported that AGPs are present in the intine wall of Quercus suber pollen grains, providing an insight into the involvement of AGPs in pollen intine formation (Costa et al, 2015). Previous studies suggested AGPs play a key role in several plant developmental processes (Du et al, 1996;van Hengel and Roberts, 2003;Park et al, 2003;Motose et al, 2004;Hu et al, 2006;Coimbra et al, 2007Coimbra et al, , 2009Coimbra et al, , 2010Yang et al, 2007;Levitin Quiapim et al, 2009;Zhong et al, 2011;Wang et al, 2015). The involvement of AGPs in pollen ontogeny has also been reported in several plant species.…”

“…Arabinogalactan proteins (AGPs) are extensively glycosylated hydroxyproline-rich glycoproteins, ubiquitous in the plant kingdom (Showalter, 2001;Dong et al, 2013). To date, 85, 69 and 149 putative AGPs have been identified in Arabidopsis, Oryza sativa and Brassica rapa, respectively (Sun et al, 2005;Mashiguchi et al, 2009;Ma and Zhao, 2010;Showalter et al, 2010;Li and Wu, 2012;Li et al, 2013;Han et al, 2017). Based on the AGP backbones and the presence of a conserved domain, AGPs in higher plants are divided into seven different subclasses, including classical AGPs, non-classical AGPs, lysine-rich AGPs, AG peptides, fasciclin-like AGPs (FLAs), xylogen-like AGPs and nodulin-like proteins (Ma et al, 2015).…”