Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta SCIE SCOPUS

DC Field Value Language
dc.contributor.author Lee, JunMo -
dc.contributor.author Yang, Eun Chan -
dc.contributor.author Graf, Louis -
dc.contributor.author Yang, Ji Hyun -
dc.contributor.author Qiu, Huan -
dc.contributor.author Zelzion, Udi -
dc.contributor.author Chan, Cheong Xin -
dc.contributor.author Stephens, Timothy G. -
dc.contributor.author Weber, Andreas P. M. -
dc.contributor.author Boo, Ga Hun -
dc.contributor.author Boo, Sung Min -
dc.contributor.author Kim, Kyeong Mi -
dc.contributor.author Shin, Younhee -
dc.contributor.author Jung, Myunghee -
dc.contributor.author Lee, Seung Jae -
dc.contributor.author Yim, Hyung-Soon -
dc.contributor.author Lee, Jung-Hyun -
dc.contributor.author Bhattacharya, Debashish -
dc.contributor.author Yoon, Hwan Su -
dc.date.accessioned 2020-04-16T08:40:21Z -
dc.date.available 2020-04-16T08:40:21Z -
dc.date.created 2020-01-28 -
dc.date.issued 2018-08 -
dc.identifier.issn 0737-4038 -
dc.identifier.uri https://sciwatch.kiost.ac.kr/handle/2020.kiost/857 -
dc.description.abstract Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high-quality 92.1 Mb draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) What is the role of repeats and transposable elements (TEs) in explaining Rhodophyta genome size variation, 2) what is the history of genome duplication and gene family expansion/reduction in these taxa, and 3) is there evidence for TE suppression in red algae? We find that the number of predicted genes in red algae is relatively small (4,803-13,125 genes), particularly when compared with land plants, with no evidence of polyploidization. Genome size variation is primarily explained by TE expansion with the red seaweeds having the largest genomes. Long terminal repeat elements and DNA repeats are the major contributors to genome size growth. About 8.3% of the G. chorda genome undergoes cytosine methylation among gene bodies, promoters, and TEs, and 71.5% of TEs contain methylated-DNA with 57% of these regions associated with sRNAs. These latter results suggest a role for TE-associated sRNAs in RNA-dependent DNA methylation to facilitate silencing. We postulate that the evolution of genome size in red algae is the result of the combined action of TE spread and the concomitant emergence of its epigenetic suppression, together with other important factors such as changes in population size. -
dc.description.uri 1 -
dc.language English -
dc.publisher OXFORD UNIV PRESS -
dc.subject DIRECTED DNA METHYLATION -
dc.subject DE-NOVO IDENTIFICATION -
dc.subject TRANSPOSABLE ELEMENTS -
dc.subject CPG-ISLANDS -
dc.subject EPIGENETIC INHERITANCE -
dc.subject GENE DUPLICATION -
dc.subject SMALL RNAS -
dc.subject HIGH LIGHT -
dc.subject C-VALUE -
dc.subject PLANTS -
dc.title Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta -
dc.type Article -
dc.citation.endPage 1886 -
dc.citation.startPage 1869 -
dc.citation.title MOLECULAR BIOLOGY AND EVOLUTION -
dc.citation.volume 35 -
dc.citation.number 8 -
dc.contributor.alternativeName 양은찬 -
dc.contributor.alternativeName 임형순 -
dc.contributor.alternativeName 이정현 -
dc.identifier.bibliographicCitation MOLECULAR BIOLOGY AND EVOLUTION, v.35, no.8, pp.1869 - 1886 -
dc.identifier.doi 10.1093/molbev/msy081 -
dc.identifier.scopusid 2-s2.0-85050180665 -
dc.identifier.wosid 000441143000004 -
dc.type.docType Article -
dc.description.journalClass 1 -
dc.subject.keywordPlus DIRECTED DNA METHYLATION -
dc.subject.keywordPlus DE-NOVO IDENTIFICATION -
dc.subject.keywordPlus TRANSPOSABLE ELEMENTS -
dc.subject.keywordPlus CPG-ISLANDS -
dc.subject.keywordPlus EPIGENETIC INHERITANCE -
dc.subject.keywordPlus GENE DUPLICATION -
dc.subject.keywordPlus SMALL RNAS -
dc.subject.keywordPlus HIGH LIGHT -
dc.subject.keywordPlus C-VALUE -
dc.subject.keywordPlus PLANTS -
dc.subject.keywordAuthor Rhodophyta -
dc.subject.keywordAuthor Gracilariopsis chorda -
dc.subject.keywordAuthor DNA methylation -
dc.subject.keywordAuthor transposable element suppression -
dc.subject.keywordAuthor small RNAs -
dc.relation.journalWebOfScienceCategory Biochemistry & Molecular Biology -
dc.relation.journalWebOfScienceCategory Evolutionary Biology -
dc.relation.journalWebOfScienceCategory Genetics & Heredity -
dc.description.journalRegisteredClass scie -
dc.description.journalRegisteredClass scopus -
dc.relation.journalResearchArea Biochemistry & Molecular Biology -
dc.relation.journalResearchArea Evolutionary Biology -
dc.relation.journalResearchArea Genetics & Heredity -
Appears in Collections:
Ocean Climate Solutions Research Division > Ocean Climate Response & Ecosystem Research Department > 1. Journal Articles
Marine Resources & Environment Research Division > Marine Biotechnology &Bioresource Research Department > 1. Journal Articles
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