Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.)

Ma, Hongwei; Jie, Zhao

doi:10.1093/jxb/erq104

Cited by 151 publications

(193 citation statements)

References 63 publications

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“…However, very little is known about the function of these genes in rice except OsWAK1, whose overexpression increased resistance to the blast fungus Magnaporthe oryzae Kohorn and Kohorn, 2012). FAS1 (for fasciclin-like) domain-containing genes are another group of transmembrane genes involved in cell adhesion (Johnson et al, 2003;Ma and Zhao, 2010). All five fasciclin domain genes in the common DEGs showed conserved down-regulation.…”

Section: Discussionmentioning

confidence: 99%

Machine Learning Approaches Distinguish Multiple Stress Conditions using Stress-Responsive Genes and Identify Candidate Genes for Broad Resistance in Rice

2013

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Abiotic and biotic stress responses are traditionally thought to be regulated by discrete signaling mechanisms. Recent experimental evidence revealed a more complex picture where these mechanisms are highly entangled and can have synergistic and antagonistic effects on each other. In this study, we identified shared stress-responsive genes between abiotic and biotic stresses in rice (Oryza sativa) by performing meta-analyses of microarray studies. About 70% of the 1,377 common differentially expressed genes showed conserved expression status, and the majority of the rest were down-regulated in abiotic stresses and up-regulated in biotic stresses. Using dimension reduction techniques, principal component analysis, and partial least squares discriminant analysis, we were able to segregate abiotic and biotic stresses into separate entities. The supervised machine learning model, recursive-support vector machine, could classify abiotic and biotic stresses with 100% accuracy using a subset of differentially expressed genes. Furthermore, using a random forests decision tree model, eight out of 10 stress conditions were classified with high accuracy. Comparison of genes contributing most to the accurate classification by partial least squares discriminant analysis, recursive-support vector machine, and random forests revealed 196 common genes with a dynamic range of expression levels in multiple stresses. Functional enrichment and coexpression network analysis revealed the different roles of transcription factors and genes responding to phytohormones or modulating hormone levels in the regulation of stress responses. We envisage the top-ranked genes identified in this study, which highly discriminate abiotic and biotic stresses, as key components to further our understanding of the inherently complex nature of multiple stress responses in plants.

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Section: Discussionmentioning

confidence: 99%

Machine Learning Approaches Distinguish Multiple Stress Conditions using Stress-Responsive Genes and Identify Candidate Genes for Broad Resistance in Rice

2013

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“…In addition to Arabidopsis, genes encoding AGPs have been found previously in rice (Oryza sativa; Ma and Zhao, 2010) and the moss Physcomitrella patens . The MAAB pipeline identified 11 GPI-AGPs in rice compared with eight in a previous study (Ma and Zhao, 2010) from similar data sets (Rice Genome Annotation Project, release 5). Differences are likely due to different percentage PAST thresholds (45% compared with 50%; data not shown).…”

Section: Evaluation Of the Maab Pipeline Using Phytozome Proteomesmentioning

confidence: 99%

“…The protein backbone of AGPs is rich in the amino acids Pro/Hyp, Ala, Ser, and Thr of PAST (Schultz et al, 2002;Ma and Zhao, 2010;Showalter et al, 2010). A biased amino acid approach (50% or greater PAST) was developed to detect Arabidopsis (Arabidopsis thaliana) AGPs (Schultz et al, 2002), which also identified some EXTs and PRPs (Johnson et al, 2003b).…”

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confidence: 99%

Pipeline to Identify Hydroxyproline-Rich Glycoproteins

et al. 2017

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Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three-dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signaling, and regulatory processes. A superfamily of cell wall proteins, the hydroxyprolinerich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive posttranslational modifications (glycosylation), and they have been implicated in many biological functions. HRGPs are evolutionarily ancient, having been isolated from the protein-rich walls of chlorophyte algae to the cellulose-rich walls of embryophytes. Examination of HRGPs in a range of plant species should provide valuable insights into how they have evolved. Commonly divided into the arabinogalactan proteins, extensins, and proline-rich proteins, in reality, a continuum of structures exists within this diverse and heterogenous superfamily. An inability to accurately classify HRGPs leads to inconsistent gene ontologies limiting the identification of HRGP classes in existing and emerging omics data sets. We present a novel and robust motif and amino acid bias (MAAB) bioinformatics pipeline to classify HRGPs into 23 descriptive subclasses. Validation of MAAB was achieved using available genomic resources and then applied to the 1000 Plants transcriptome project (www.onekp.com) data set. Significant improvement in the detection of HRGPs using multiple-kmer transcriptome assembly methodology was observed. The MAAB pipeline is readily adaptable and can be modified to optimize the recovery of IDPs from other organisms.

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“…Two genes would be regarded as tandem duplications if there were less than five genes between these two genes (Ma and Zhao 2010). The definition of segmental duplication was as reported in a previous study (Maher et al 2006).…”

Section: Chromosomal Location and Duplication Model Of Caleosin Genesmentioning

confidence: 99%

Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

et al. 2016

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Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions? Contact the NRC Publications Archive team atPublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. NRC Publications Record / Notice d'Archives des publications de CNRC:http://nparc.cisti-icist.nrc-cnrc.gc.ca/eng/view/object/?id=f37a8f5d-b46d-49f5-ba0f-e42c14b87a96 http://nparc.cisti-icist.nrc-cnrc.gc.ca/fra/voir/objet/?id=f37a8f5d-b46d-49f5-ba0f-e42c14b87a96 the first time. Segmental duplication was the main form of gene expansion. Alignment, motif and phylogenetic analyses showed that Brassica caleosins belong to either the H-family or the L-family with different motif structures and physicochemical properties. Our findings strongly suggest that L-caleosins are evolved from H-caleosins. Predicted phosphorylation sites were differentially conserved in H-caleosin and L-caleosins, respectively. 'RY-repeat' elements and phytohormone-related cis-elements were identified in different caleosins, which suggest diverse physiological functions. Gene structure analysis indicated that most caleosins (38 out of 44) contained six exons and five introns and their intron phases were highly conserved. Structurally integrated caleosins, such as BrCLO3-3 and BrCLO4-2, showed high expression levels and may have important roles. Some caleosins, such as BrCLO2 and BoCLO8-2, lost motifs of the calcium binding domain, proline knot, potential phosphorylation sites and haem-binding sites. Combined with their low expression, it is suggested that these caleosins may have lost function. 1 3 Mol Genet Genomics DOI 10.1007/s00438-015-1156- Abstract

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Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.)

Cited by 151 publications

References 63 publications

Machine Learning Approaches Distinguish Multiple Stress Conditions using Stress-Responsive Genes and Identify Candidate Genes for Broad Resistance in Rice

Machine Learning Approaches Distinguish Multiple Stress Conditions using Stress-Responsive Genes and Identify Candidate Genes for Broad Resistance in Rice

Pipeline to Identify Hydroxyproline-Rich Glycoproteins

Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

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