Lee, JunMo, Yang, Eun Chan ORCID: 0000-0001-8211-8130, Graf, Louis ORCID: 0000-0001-8276-1687, Yang, Ji Hyun, Qiu, Huan, Zelzion, Udi, Chan, Cheong Xin ORCID: 0000-0002-3729-8176, Stephens, Timothy G., Weber, Andreas P. M., Boo, Ga Hun ORCID: 0000-0002-3019-2678, Boo, Sung Min, Kim, Kyeong Mi, Shin, Younhee, Jung, Myunghee, Lee, Seung Jae, Yim, Hyung-Soon, Lee, Jung-Hyun, Bhattacharya, Debashish and Yoon, Hwan Su (2018). Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta. Mol. Biol. Evol., 35 (8). S. 1869 - 1887. OXFORD: OXFORD UNIV PRESS. ISSN 1537-1719

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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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Lee, JunMoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yang, Eun ChanUNSPECIFIEDorcid.org/0000-0001-8211-8130UNSPECIFIED
Graf, LouisUNSPECIFIEDorcid.org/0000-0001-8276-1687UNSPECIFIED
Yang, Ji HyunUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Qiu, HuanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zelzion, UdiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chan, Cheong XinUNSPECIFIEDorcid.org/0000-0002-3729-8176UNSPECIFIED
Stephens, Timothy G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Weber, Andreas P. M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Boo, Ga HunUNSPECIFIEDorcid.org/0000-0002-3019-2678UNSPECIFIED
Boo, Sung MinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kim, Kyeong MiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shin, YounheeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jung, MyungheeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lee, Seung JaeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yim, Hyung-SoonUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lee, Jung-HyunUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bhattacharya, DebashishUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yoon, Hwan SuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-177391
DOI: 10.1093/molbev/msy081
Journal or Publication Title: Mol. Biol. Evol.
Volume: 35
Number: 8
Page Range: S. 1869 - 1887
Date: 2018
Publisher: OXFORD UNIV PRESS
Place of Publication: OXFORD
ISSN: 1537-1719
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
DIRECTED DNA METHYLATION; DE-NOVO IDENTIFICATION; TRANSPOSABLE ELEMENTS; CPG-ISLANDS; EPIGENETIC INHERITANCE; GENE DUPLICATION; SMALL RNAS; HIGH LIGHT; C-VALUE; PLANTSMultiple languages
Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & HeredityMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/17739

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