In silico identification and characterisation of 17 polymorphic anonymous non-coding sequence markers (ANMs) for red grouse (Lagopus lagopus scotica)

被引：2

作者：

Wenzel, Marius A. ^{[1
]}

Piertney, Stuart B. ^{[1
]}

机构：

[1] Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen AB24 2TZ, Scotland

来源：

CONSERVATION GENETICS RESOURCES | 2015年 / 7卷 / 02期

基金：

英国生物技术与生命科学研究理事会;

关键词：

Anonymous nuclear markers; Non-coding DNA; Neutral evolution; Red grouse; Lagopus; NUCLEAR MARKERS; PHYLOGEOGRAPHY; DATABASE; ECOLOGY; BLAST;

D O I：

10.1007/s12686-014-0416-0

中图分类号：

X176 [生物多样性保护];

学科分类号：

090705 ;

摘要：

Anonymous non-coding sequence markers (ANMs) are powerful neutral genetic markers with great utility in phylogeography, population genetics and population genomics. Developing ANMs has previously relied on sequencing random fragments of genomic DNA in the target species and then querying bioinformatics databases to identify unannotated, putatively neutral fragments. Here, we describe an alternative in silico approach that is based on identifying large unannotated genomic regions in model species to provide a priori neutral targets for candidate ANMs that are remote from exonic regions. We illustrate this approach by developing a set of 17 polymorphic ANMs for red grouse (Lagopus lagopus scotica) from c. 1 Mbp non-coding chromosome regions of chicken, turkey and zebrafinch genomes. This pipeline presents a powerful and efficient approach when appropriate model genomes are available for the target species of interest.

引用

页码：319 / 323

页数：5

共 20 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2]

[Anonymous], GENEIOUS V5 6 3

[3] Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome [J].

Backstroem, Niclas ;

Fagerberg, Sofie ;

Ellegren, Hans .

MOLECULAR ECOLOGY, 2008, 17 (04) :964-980

[4] Anonymous nuclear markers for the African adders (Serpentes: Viperidae: Bitis) [J].

Barlow, Axel ;

Grail, Wendy ;

de Bruyn, Mark ;

Wuester, Wolfgang .

CONSERVATION GENETICS RESOURCES, 2012, 4 (04) :967-969

[5] Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys [J].

Bertozzi, Terry ;

Sanders, Kate L. ;

Sistrom, Mark J. ;

Gardner, Michael G. .

BIOINFORMATICS, 2012, 28 (14) :1807-1810

[6] Multilocus phylogeography and phylogenetics using sequence-based markers [J].

Brito, Patricia H. ;

Edwards, Scott V. .

GENETICA, 2009, 135 (03) :439-455

[7] The UCSC Genome Browser Database: update 2006 [J].

Hinrichs, A. S. ;

Karolchik, D. ;

Baertsch, R. ;

Barber, G. P. ;

Bejerano, G. ;

Clawson, H. ;

Diekhans, M. ;

Furey, T. S. ;

Harte, R. A. ;

Hsu, F. ;

Hillman-Jackson, J. ;

Kuhn, R. M. ;

Pedersen, J. S. ;

Pohl, A. ;

Raney, B. J. ;

Rosenbloom, K. R. ;

Siepel, A. ;

Smith, K. E. ;

Sugnet, C. W. ;

Sultan-Qurraie, A. ;

Thomas, D. J. ;

Trumbower, H. ;

Weber, R. J. ;

Weirauch, M. ;

Zweig, A. S. ;

Haussler, D. ;

Kent, W. J. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D590-D598

[8] The UCSC Table Browser data retrieval tool [J].

Karolchik, D ;

Hinrichs, AS ;

Furey, TS ;

Roskin, KM ;

Sugnet, CW ;

Haussler, D ;

Kent, WJ .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D493-D496

[9]

Kent WJ, 2002, GENOME RES, V12, P656, DOI [10.1101/gr.229202. Article published online before March 2002, 10.1101/gr.229202]

[10] DIVERGENCE ACROSS AUSTRALIA'S CARPENTARIAN BARRIER: STATISTICAL PHYLOGEOGRAPHY OF THE RED-BACKED FAIRY WREN(MALURUS MELANOCEPHALUS) [J].

Lee, June Y. ;

Edwards, Scott V. .

EVOLUTION, 2008, 62 (12) :3117-3134

← 1 2 →