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Rapid Identification of Major Histocompatibility Complex Class I Haplotypes Using Deep Sequencing in an Endangered Old World Monkey. 濒危旧大陆猴主要组织相容性复合体I类单倍型的深度测序快速鉴定
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2016-03-01 Epub Date: 2016-01-22 DOI: 10.1007/s12686-016-0516-0
Noah D Simons, Maria Jose Ruiz-Lopez, Colin A Chapman, Tony L Goldberg, Julie A Karl, Roger W Wiseman, Patrick S Bohn, David H O'Connor, Nelson Ting
{"title":"Rapid Identification of Major Histocompatibility Complex Class I Haplotypes Using Deep Sequencing in an Endangered Old World Monkey.","authors":"Noah D Simons,&nbsp;Maria Jose Ruiz-Lopez,&nbsp;Colin A Chapman,&nbsp;Tony L Goldberg,&nbsp;Julie A Karl,&nbsp;Roger W Wiseman,&nbsp;Patrick S Bohn,&nbsp;David H O'Connor,&nbsp;Nelson Ting","doi":"10.1007/s12686-016-0516-0","DOIUrl":"https://doi.org/10.1007/s12686-016-0516-0","url":null,"abstract":"<p><p>Immunogenetic data from wild primate populations have been difficult to obtain, due to logistic and methodological constraints. We applied a well-characterized deep sequencing method for MHC I typing, developed for macaques, to a population of wild red colobus to assess the feasibility of identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data from blood and tissue samples to assign haplotypes. Eighty-two sequences were classified as red colobus MHC I alleles distributed across six MHC I loci. Individuals averaged ~13k reads across six MHC I loci, with 83% of all alleles representing either MHC I-A or MHC I-B loci. This study not only represents an important advance in the identification and genotyping of MHC in the endangered red colobus but also shows the potential for using this approach in other endangered wild primates.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"8 1","pages":"23-26"},"PeriodicalIF":1.1,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-016-0516-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34394176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data. 基于Illumina下一代测序数据的优化、流线型微卫星开发的基于星系的生物信息学管道。
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2016-01-01 Epub Date: 2016-08-02 DOI: 10.1007/s12686-016-0570-7
Sarah M Griffiths, Graeme Fox, Peter J Briggs, Ian J Donaldson, Simon Hood, Pen Richardson, George W Leaver, Nathan K Truelove, Richard F Preziosi
{"title":"A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data.","authors":"Sarah M Griffiths,&nbsp;Graeme Fox,&nbsp;Peter J Briggs,&nbsp;Ian J Donaldson,&nbsp;Simon Hood,&nbsp;Pen Richardson,&nbsp;George W Leaver,&nbsp;Nathan K Truelove,&nbsp;Richard F Preziosi","doi":"10.1007/s12686-016-0570-7","DOIUrl":"https://doi.org/10.1007/s12686-016-0570-7","url":null,"abstract":"<p><p>Microsatellites are useful tools for ecologists and conservationist biologists, but are taxa-specific and traditionally expensive and time-consuming to develop. New methods using next-generation sequencing (NGS) have reduced these problems, but the plethora of software available for processing NGS data may cause confusion and difficulty for researchers new to the field of bioinformatics. We developed a bioinformatics pipeline for microsatellite development from Illumina paired-end sequences, which is packaged in the open-source bioinformatics tool Galaxy. This optimises and streamlines the design of a microsatellite panel and provides a user-friendly graphical user interface. The pipeline utilises existing programs along with our own novel program and wrappers to: quality-filter and trim reads (Trimmomatic); generate sequence quality reports (FastQC); identify potentially-amplifiable microsatellite loci (Pal_finder); design primers (Primer3); assemble pairs of reads to enhance marker amplification success rates (PANDAseq); and filter optimal loci (Pal_filter). The complete pipeline is freely available for use via a pre-configured Galaxy instance, accessible at https://palfinder.ls.manchester.ac.uk.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"8 4","pages":"481-486"},"PeriodicalIF":1.1,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-016-0570-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37890616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 35
Diagnostic single nucleotide polymorphism markers to identify hybridization between dromedary and Bactrian camels. 诊断单核苷酸多态性标记鉴定单峰骆驼和双峰驼杂交。
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2015-01-01 Epub Date: 2015-01-13 DOI: 10.1007/s12686-015-0420-z
Emily Ruiz, Elmira Mohandesan, Robert R Fitak, Pamela A Burger
{"title":"Diagnostic single nucleotide polymorphism markers to identify hybridization between dromedary and Bactrian camels.","authors":"Emily Ruiz,&nbsp;Elmira Mohandesan,&nbsp;Robert R Fitak,&nbsp;Pamela A Burger","doi":"10.1007/s12686-015-0420-z","DOIUrl":"https://doi.org/10.1007/s12686-015-0420-z","url":null,"abstract":"<p><p>The technique to produce hybrid <i>Tulu</i> or <i>Nar</i> camels from crosses between dromedary and Bactrian camels is common throughout Middle Eastern and Central Asian countries. Formerly, these hybrids were highly valued as strong and persistent pack animals but today are bred to improve milk or wool quality in the respective species and for camel wrestling. We developed a diagnostic single nucleotide polymorphism (SNP) panel to identify cryptic ancestry in F<sub>1</sub> hybrids and their backcrosses by selecting loci from whole genome data, which were fixed for different alleles in either dromedary or domestic and wild Bactrian camel. With this SNP panel we are able to identify the hybridization patterns in camels with uncertain origins, support hybrid breeding management and to detect potential rare dromedary introgression in the last wild Bactrian camels in Mongolia and China.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"7 2","pages":"329-332"},"PeriodicalIF":1.1,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-015-0420-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34276364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Development of 14 microsatellite markers in the Queensland koala (Phascolarctos cinereus adustus) using next generation sequencing technology. 利用下一代测序技术在昆士兰考拉(Phascolarctos cinereus adusstus)中开发14个微卫星标记。
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2014-06-01 DOI: 10.1007/s12686-013-0115-2
Christina T Ruiz-Rodriguez, Yasuko Ishida, Alex D Greenwood, Alfred L Roca
{"title":"Development of 14 microsatellite markers in the Queensland koala (<i>Phascolarctos cinereus adustus</i>) using next generation sequencing technology.","authors":"Christina T Ruiz-Rodriguez,&nbsp;Yasuko Ishida,&nbsp;Alex D Greenwood,&nbsp;Alfred L Roca","doi":"10.1007/s12686-013-0115-2","DOIUrl":"https://doi.org/10.1007/s12686-013-0115-2","url":null,"abstract":"<p><p>We report the development of 14 new microsatellite markers in the Queensland koala (<i>Phascolarctos cinereus adustus</i>). Ten unrelated Queensland koala individuals from the San Diego Zoo, USA, were genotyped. The number of alleles per locus ranged from 2 to 7, with an average of 5.14 alleles per locus. Across all loci, the average observed and expected heterozygosity values were both 0.69. These polymorphic microsatellite loci will be useful for genetic studies relevant to the conservation of the koala, a species listed as vulnerable.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"6 2","pages":"429-431"},"PeriodicalIF":1.1,"publicationDate":"2014-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-013-0115-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32539404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 16
Development of microsatellite markers in Robinsonia (Asteraceae) an endemic genus of the Juan Fernández Archipelago, Chile. 智利胡安Fernández群岛特有属鲁宾逊(Asteraceae)微卫星标记的开发。
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2013-03-01 Epub Date: 2012-08-19 DOI: 10.1007/s12686-012-9734-2
Koji Takayama, Patricio López Sepúlveda, Gudrun Kohl, Johannes Novak, Tod F Stuessy
{"title":"Development of microsatellite markers in <i>Robinsonia</i> (Asteraceae) an endemic genus of the Juan Fernández Archipelago, Chile.","authors":"Koji Takayama,&nbsp;Patricio López Sepúlveda,&nbsp;Gudrun Kohl,&nbsp;Johannes Novak,&nbsp;Tod F Stuessy","doi":"10.1007/s12686-012-9734-2","DOIUrl":"https://doi.org/10.1007/s12686-012-9734-2","url":null,"abstract":"<p><p>Ten microsatellite markers were developed for <i>Robinsonia</i> (Asteraceae), a genus endemic to the Juan Fernández Archipelago, Chile. Polymorphisms of these markers were tested using one population each of <i>R. evenia</i>, <i>R. gayana</i>, and <i>R. gracilis</i>. The number of alleles for these markers ranged from 2 to 17 per locus, and expected heterozygosity ranged from 0 to 0.847 by population. A significant deviation from Hardy-Weinberg equilibrium was observed in zero to two markers in each population, and no significant linkage disequilibrium between markers was detected. The markers reported here would be useful for evolutionary studies and conservation strategies in <i>Robinsonia</i>.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"5 1","pages":"63-67"},"PeriodicalIF":1.1,"publicationDate":"2013-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-012-9734-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31272182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
17 novel polymorphic microsatellite markers for the giant water bug, Abedus herberti (Belostomatidae). 巨型水虫Abedus herberti的17个新的多态微卫星标记。
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2012-12-01 DOI: 10.1007/s12686-012-9687-5
T S Daly-Engel, R L Smith, D S Finn, M E Knoderbane, I C Phillipsen, D A Lytle
{"title":"17 novel polymorphic microsatellite markers for the giant water bug, <i>Abedus herberti</i> (Belostomatidae).","authors":"T S Daly-Engel,&nbsp;R L Smith,&nbsp;D S Finn,&nbsp;M E Knoderbane,&nbsp;I C Phillipsen,&nbsp;D A Lytle","doi":"10.1007/s12686-012-9687-5","DOIUrl":"https://doi.org/10.1007/s12686-012-9687-5","url":null,"abstract":"<p><p>The giant water bug (<i>Abedus herberti</i>) is a large flightless insect that is a keystone predator in aridland aquatic habitats. Extended droughts, possibly due to climate change and groundwater pumping, are causing once-perennial aquatic habitats to dry, resulting in serious conservation concern for some populations. <i>A. herberti</i> also exhibits exclusive male parental care, which has made it a model organism for studying mating systems evolution. Here we describe 17 novel polymorphic microsatellite loci developed for <i>A. herberti</i>. Number of alleles per locus ranged from 2 to 15, and average observed and expected heterozygosities were 0.579 and 0.697, respectively. These loci can successfully resolve both population genetic structure among sites separated by 3-100 km (<i>F</i><sub>ST</sub> = 0.08-0.21, <i>P</i> < 0.0001), and divergent mating strategies within local populations, making them highly useful for conservation genetics studies of this vulnerable species.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"4 4","pages":"979-981"},"PeriodicalIF":1.1,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-012-9687-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31768255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
PolyAna: analyzing synonymous and nonsynonymous polymorphic sites. PolyAna:分析同义和非同义多态位点。
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2011-07-01 DOI: 10.1007/s12686-010-9372-5
Ethan W Knapp, Stephanie Jiménez Irausquin, Robert Friedman, Austin L Hughes
{"title":"PolyAna: analyzing synonymous and nonsynonymous polymorphic sites.","authors":"Ethan W Knapp,&nbsp;Stephanie Jiménez Irausquin,&nbsp;Robert Friedman,&nbsp;Austin L Hughes","doi":"10.1007/s12686-010-9372-5","DOIUrl":"https://doi.org/10.1007/s12686-010-9372-5","url":null,"abstract":"<p><p>PolyAna (available at http://www.biol.sc.edu/~austin/) aids in the analysis of natural selection on protein-coding sequences by estimating sample gene diversity at individual polymorphic nucleotide sites, which are classified as synonymous, non-synonymous, or ambiguous.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"3 3","pages":"429-431"},"PeriodicalIF":1.1,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-010-9372-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29985986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Development and characterization of microsatellite markers in Sarracenia L. (pitcher plant) species. 猪笼草(Sarracenia L.)微卫星标记的开发与鉴定。
IF 1.1 4区 环境科学与生态学
Conservation Genetics Resources Pub Date : 2010-12-01 DOI: 10.1007/s12686-009-9165-x
Willie L Rogers, Jennifer M Cruse-Sanders, Ron Determann, Russell L Malmberg
{"title":"Development and characterization of microsatellite markers in Sarracenia L. (pitcher plant) species.","authors":"Willie L Rogers,&nbsp;Jennifer M Cruse-Sanders,&nbsp;Ron Determann,&nbsp;Russell L Malmberg","doi":"10.1007/s12686-009-9165-x","DOIUrl":"https://doi.org/10.1007/s12686-009-9165-x","url":null,"abstract":"<p><p>Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. Sarracenia species naturally hybridize with each other, and hybrid swarms have been identified. A number of the taxa within the genus are considered endangered. In order to facilitate evolutionary, ecological and conservation genetic analyses within the genus, we developed 25 microsatellite loci which show variability either within species or between species. Three S. purpurea populations were examined with 10 primer sets which showed within population variability.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"2 1","pages":"75-79"},"PeriodicalIF":1.1,"publicationDate":"2010-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12686-009-9165-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29545687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
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