Mining of EST-SSR from 454 pyrosequencing in the surf clam Mesodesma donacium (Lamark, 1818)

被引：6

作者：

Aguilar-Espinoza, A. ^{[1
]}

Guzman-Riffo, B. ^{[1
]}

Haye, P. A. ^{[2
,3
]}

Gallardo-Escarate, C. ^{[1
]}

机构：

[1] Univ Concepcion, Ctr Biotecnol, Dept Oceanog, Lab Biotecnol & Genom Acuicola, Concepcion, Chile

[2] Univ Catolica Norte, Fac Ciencias Mar, Dept Biol Marina, Lab Diversidad Mol, Coquimbo, Chile

[3] Ctr Estudios Avanzados Zonas Aridas, Coquimbo, Chile

来源：

CONSERVATION GENETICS RESOURCES | 2012年 / 4卷 / 04期

关键词：

Pyrosequencing; 454; Expressed sequence tag (EST); Microsatellite; Mesodesma donacium; MICROSATELLITE MARKERS; UNIVERSAL; PROGRAM;

D O I：

10.1007/s12686-012-9652-3

中图分类号：

X176 [生物多样性保护];

学科分类号：

090705 ;

摘要：

Novel simple sequence repeats (SSR) were identified from 454 transcriptome pyrosequencing ESTs in the surf clam Mesodesma donacium. From 7,734 ESTs annotated with SSR motives, 75 putative EST-SSRs were selected according their repetitive DNA sequence and functional annotation (Gene ontology), of these, 15 were characterized on 45 individuals of two wild populations located in two different biogeographic transition zones of the coast of Chile (30 and 42A degrees S). Most loci were in Hardy-Weinberg equilibrium, and the polymorphic information content (PIC) ranged from 0.243 to 0.634. Pairwise F (st) between sampled populations was estimated in 0.478. These EST-SSR markers promise to be useful for future management strategies of this overexploited species.

引用

页码：829 / 832

页数：4

共 19 条

[1] Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques [J].

Aljanabi, SM ;

Martinez, I .

NUCLEIC ACIDS RESEARCH, 1997, 25 (22) :4692-4693

[2] Blast2GO:: a universal tool for annotation, visualization and analysis in functional genomics research [J].

Conesa, A ;

Götz, S ;

García-Gómez, JM ;

Terol, J ;

Talón, M ;

Robles, M .

BIOINFORMATICS, 2005, 21 (18) :3674-3676

[3] Genome-wide genetic marker discovery and genotyping using next-generation sequencing [J].

Davey, John W. ;

Hohenlohe, Paul A. ;

Etter, Paul D. ;

Boone, Jason Q. ;

Catchen, Julian M. ;

Blaxter, Mark L. .

NATURE REVIEWS GENETICS, 2011, 12 (07) :499-510

[4] Arlequin (version 3.0): An integrated software package for population genetics data analysis [J].

Excoffier, Laurent ;

Laval, Guillaume ;

Schneider, Stefan .

EVOLUTIONARY BIOINFORMATICS, 2005, 1 :47-50

[5] FSTAT (Version 1.2): A computer program to calculate F-statistics [J].

Goudet, J .

JOURNAL OF HEREDITY, 1995, 86 (06) :485-486

[6] Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat [J].

Gupta, PK ;

Rustgi, S ;

Sharma, S ;

Singh, R ;

Kumar, N ;

Balyan, HS .

MOLECULAR GENETICS AND GENOMICS, 2003, 270 (04) :315-323

[7] Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment [J].

Kalinowski, Steven T. ;

Taper, Mark L. ;

Marshall, Tristan C. .

MOLECULAR ECOLOGY, 2007, 16 (05) :1099-1106

[8] Identification of host-defense genes and development of microsatellite markers from ESTs of hard clam Meretrix meretrix [J].

Li, Hong-jun ;

Liu, Wei-dong ;

Gao, Xiang-gang ;

Zhu, Dan ;

Wang, Juan ;

Li, Yun-feng ;

He, Chong-bo .

MOLECULAR BIOLOGY REPORTS, 2011, 38 (02) :769-775

[9] Development of expressed sequence tag-derived microsatellite markers for Saccharina (Laminaria) japonica [J].

Liu, Fuli ;

Wang, Xiuliang ;

Yao, Jianting ;

Fu, Wandong ;

Duan, Delin .

JOURNAL OF APPLIED PHYCOLOGY, 2010, 22 (01) :109-111

[10] High genetic distance between marine bivalves of the genus Mesodesma inhabiting the Atlantic and Pacific coasts of South America [J].

Marins, LF ;

Levy, JA .

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR AND INTEGRATIVE PHYSIOLOGY, 1999, 124 (03) :313-319

← 1 2 →