Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome

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	Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome
	Wang, Hongxia; Huan, Pin; Lu, Xia; Liu, Baozhong
	2011-06-01
发表期刊	GENES & GENETIC SYSTEMS
ISSN	1341-7568
卷号	86 期号:3 页码:197-205
文章类型	Article
摘要	A total of 2,970 EST-SSRs (2.38%) were identified by transcriptome sequencing of clam Meretrix meretrix (751,970 reads, similar to 310.82 Mbp), using 454 Genome Sequencer FLX next-generation sequencing platform. Dinucleotide SSR was the dominant repeat type (40.2%), followed by trinucleotide (37.8%), tetranuleotide (12.0%) and pentanucleotide (2.0%) SSR. The dominant repeat motif was AT (71.3%) in the dinucleotide SSR type and AAC (45.6%) in the trinucleotide SSR type. Nearly 79% of all microsatellites had flanking sequences suitable for PCR primer design. Half of PAL were found to be polymorphic in a subset of 40 primer pairs randomly selected. Specifically, the density of dinucleotide, trinucleotide and tetranucleotide repeats showed significant variation among four development stages (trochophore, D-veliger, pediveliger and postlarva). The results suggested that dinucleotide, trinucleotide and tetranucleotide SSRs may play an important role in contributing to the different expression profiles in larval stages.; A total of 2,970 EST-SSRs (2.38%) were identified by transcriptome sequencing of clam Meretrix meretrix (751,970 reads, similar to 310.82 Mbp), using 454 Genome Sequencer FLX next-generation sequencing platform. Dinucleotide SSR was the dominant repeat type (40.2%), followed by trinucleotide (37.8%), tetranuleotide (12.0%) and pentanucleotide (2.0%) SSR. The dominant repeat motif was AT (71.3%) in the dinucleotide SSR type and AAC (45.6%) in the trinucleotide SSR type. Nearly 79% of all microsatellites had flanking sequences suitable for PCR primer design. Half of PAL were found to be polymorphic in a subset of 40 primer pairs randomly selected. Specifically, the density of dinucleotide, trinucleotide and tetranucleotide repeats showed significant variation among four development stages (trochophore, D-veliger, pediveliger and postlarva). The results suggested that dinucleotide, trinucleotide and tetranucleotide SSRs may play an important role in contributing to the different expression profiles in larval stages.
关键词	High-throughput Marker Identification Est-ssr Developmental Stages Meretrix Meretrix
学科领域	Biochemistry & Molecular Biology ; Genetics & Heredity
收录类别	SCI
语种	英语
WOS记录号	WOS:000297428200006
引用统计	被引频次：21[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/11897
专题	实验海洋生物学重点实验室
作者单位	Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
第一作者单位	实验海洋生物学重点实验室
推荐引用方式 GB/T 7714	Wang, Hongxia,Huan, Pin,Lu, Xia,et al. Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome[J]. GENES & GENETIC SYSTEMS,2011,86(3):197-205.
APA	Wang, Hongxia,Huan, Pin,Lu, Xia,&Liu, Baozhong.(2011).Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome.GENES & GENETIC SYSTEMS,86(3),197-205.
MLA	Wang, Hongxia,et al."Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome".GENES & GENETIC SYSTEMS 86.3(2011):197-205.

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