Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae

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	Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae
	Zhao, Zhixin ; Guo, Cheng ; Sutharzan, Sreeskandarajan ; Li, Pei ; Echt, Craig S. ; Zhang, Jie ; Liang, Chun ; Li P(李培)
刊名	http://dx.doi.org/10.1534/g3.113.008524
	2014
关键词	SIMPLE SEQUENCE REPEATS ARABIDOPSIS-THALIANA EUKARYOTIC GENOMES GENE-REGULATION DNA-SEQUENCES SSR MARKERS MICROSATELLITES EVOLUTION IDENTIFICATION TRANSCRIPTION
英文摘要	NIH-AREA [1R15GM94732-1 A1]; Botany Department and Office for the Advancement of Research and Scholarship (OARS) of Miami University in Ohio; Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among the 31 species, no significant correlation was detected between the TR density and genome size. Interestingly, green alga Chlamydomonas reinhardtii (42,059 bp/Mbp) and castor bean Ricinus communis (55,454 bp/Mbp) showed much higher TR densities than all other species (13,209 bp/Mbp on average). In the 29 land plants, including 22 dicots, 5 monocots, and 2 bryophytes, 5 '-UTR and upstream intergenic 200-nt (UI200) regions had the first and second highest TR densities, whereas in the two green algae (C. reinhardtii and Volvox carteri) the first and second highest densities were found in intron and coding sequence (CDS) regions, respectively. In CDS regions, trinucleotide and hexanucleotide motifs were those most frequently represented in all species. In intron regions, especially in the two green algae, significantly more TRs were detected near the intron-exon junctions. Within intergenic regions in dicots and monocots, more TRs were found near both the 5 ' and 3 ' ends of genes. GO annotation in two green algae revealed that the genes with TRs in introns are significantly involved in transcriptional and translational processing. As the first systematic examination of TRs in plant and green algal genomes, our study showed that TRs displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation in plants and green algae.
语种	英语
出版者	GENETICS SOC AM
内容类型	期刊论文
源URL	[http://dspace.xmu.edu.cn/handle/2288/92763]
专题	信息技术－已发表论文
推荐引用方式 GB/T 7714	Zhao, Zhixin,Guo, Cheng,Sutharzan, Sreeskandarajan,et al. Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae[J]. http://dx.doi.org/10.1534/g3.113.008524,2014.
APA	Zhao, Zhixin.,Guo, Cheng.,Sutharzan, Sreeskandarajan.,Li, Pei.,Echt, Craig S..,...&李培.(2014).Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae.http://dx.doi.org/10.1534/g3.113.008524.
MLA	Zhao, Zhixin,et al."Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae".http://dx.doi.org/10.1534/g3.113.008524 (2014).