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dc.contributor.authorLiu, Xiao
dc.contributor.authorWolfe, Richard
dc.contributor.authorWelch, Lonnie R.
dc.contributor.authorDomozych, David S.
dc.contributor.authorPopper, Zoë A.
dc.contributor.authorShowalter, Allan M.
dc.date.accessioned2018-09-20T16:14:46Z
dc.date.available2018-09-20T16:14:46Z
dc.date.issued2016-02-26
dc.identifier.citationLiu, Xiao; Wolfe, Richard; Welch, Lonnie R. Domozych, David S.; Popper, Zoë A.; Showalter, Allan M. (2016). Bioinformatic identification and analysis of extensins in the plant kingdom. PLOS ONE 11 (2),
dc.identifier.issn1932-6203
dc.identifier.urihttp://hdl.handle.net/10379/12476
dc.description.abstractExtensins (EXTs) are a family of plant cell wall hydroxyproline-rich glycoproteins (HRGPs) that are implicated to play important roles in plant growth, development, and defense. Structurally, EXTs are characterized by the repeated occurrence of serine (Ser) followed by three to five prolines (Pro) residues, which are hydroxylated as hydroxyproline (Hyp) and glycosylated. Some EXTs have Tyrosine (Tyr)-X-Tyr (where X can be any amino acid) motifs that are responsible for intramolecular or intermolecular cross-linkings. EXTs can be divided into several classes: classical EXTs, short EXTs, leucine-rich repeat extensins (LRXs), proline-rich extensin-like receptor kinases (PERKs), formin-homolog EXTs (FH EXTs), chimeric EXTs, and long chimeric EXTs. To guide future research on the EXTs and understand evolutionary history of EXTs in the plant kingdom, a bioinformatics study was conducted to identify and classify EXTs from 16 fully sequenced plant genomes, including Ostreococcus lucimarinus, Chlamydomonas reinhardtii, Volvox carteri, Klebsormidium flaccidum, Physcomitrella patens, Selaginella moellendorffii, Pinus taeda, Picea abies, Brachypodium distachyon, Zea mays, Oryza sativa, Glycine max, Medicago truncatula, Brassica rapa, Solanum lycopersicum, and Solanum tuberosum, to supplement data previously obtained from Arabidopsis thaliana and Populus trichocarpa. A total of 758 EXTs were newly identified, including 87 classical EXTs, 97 short EXTs, 61 LRXs, 75 PERKs, 54 FH EXTs, 38 long chimeric EXTs, and 346 other chimeric EXTs. Several notable findings were made: (1) classical EXTs were likely derived after the terrestrialization of plants; (2) LRXs, PERKs, and FHs were derived earlier than classical EXTs; (3) monocots have few classical EXTs; (4) Eudicots have the greatest number of classical EXTs and Tyr-X-Tyr cross-linking motifs are predominantly in classical EXTs; (5) green algae have no classical EXTs but have a number of long chimeric EXTs that are absent in embryophytes. Furthermore, phylogenetic analysis was conducted of LRXs, PERKs and FH EXTs, which shed light on the evolution of three EXT classes.
dc.publisherPublic Library of Science (PLoS)
dc.relation.ispartofPLOS ONE
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Ireland
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/3.0/ie/
dc.subjectleucine-rich repeat
dc.subjectalgal prolyl 4-hydroxylase
dc.subjectcell-wall proteins
dc.subjectarabidopsis-thaliana
dc.subjectgene family
dc.subjectgenome sequence
dc.subjectproline-rich
dc.subjectvolvox-carteri
dc.subjectgreen-alga
dc.subjectmolecular characterization
dc.titleBioinformatic identification and analysis of extensins in the plant kingdom
dc.typeArticle
dc.identifier.doi10.1371/journal.pone.0150177
dc.local.publishedsourcehttps://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0150177&type=printable
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