Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies

Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies

Transcriptome-wide targeted genotyping is highly attractive for evolutionary and ecological studies but, until recently, accomplishing this goal presented a major technical barrier for the study of non-model organisms. Our group has recently developed a high-throughput targeted genotyping approach (...

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Main Authors: Xuan Zhu, Jing Wang, Jia Lv, Pingping Liu, Lingling Zhang, Wenqian Jiao, Cen Ma, Zhenmin Bao, Shi Wang
Format: Article
Language:English
Published: SAGE Publishing 2019-03-01
Series:Evolutionary Bioinformatics
Online Access:https://doi.org/10.1177/1176934319836074
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spelling doaj-feef4dd39b25486680a9c411b045ba622020-11-25T01:27:33ZengSAGE PublishingEvolutionary Bioinformatics1176-93432019-03-011510.1177/1176934319836074Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological StudiesXuan Zhu0Jing Wang1Jia Lv2Pingping Liu3Lingling Zhang4Wenqian Jiao5Cen Ma6Zhenmin Bao7Shi Wang8MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaLaboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaLaboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaLaboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaLaboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaLaboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaTranscriptome-wide targeted genotyping is highly attractive for evolutionary and ecological studies but, until recently, accomplishing this goal presented a major technical barrier for the study of non-model organisms. Our group has recently developed a high-throughput targeted genotyping approach (called HD-Marker) based on the high specificity and accuracy of oligo extension-ligation assays that facilitates the design of assays tailored to meet specific genotyping needs. HD-Marker allows for targeted genotyping of over 10 000 genes in a single tube, with strikingly high capture rate (98%-99%) and genotyping accuracy (97%-99%). With the remarkable advantages of cost-effectiveness and flexibility, we envision that HD-Marker has broad application potential in evolutionary and ecological studies.https://doi.org/10.1177/1176934319836074
collection DOAJ
language English
format Article
sources DOAJ
author Xuan Zhu
Jing Wang
Jia Lv
Pingping Liu
Lingling Zhang
Wenqian Jiao
Cen Ma
Zhenmin Bao
Shi Wang
spellingShingle Xuan Zhu
Jing Wang
Jia Lv
Pingping Liu
Lingling Zhang
Wenqian Jiao
Cen Ma
Zhenmin Bao
Shi Wang
Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies
Evolutionary Bioinformatics
author_facet Xuan Zhu
Jing Wang
Jia Lv
Pingping Liu
Lingling Zhang
Wenqian Jiao
Cen Ma
Zhenmin Bao
Shi Wang
author_sort Xuan Zhu
title Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies
title_short Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies
title_full Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies
title_fullStr Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies
title_full_unstemmed Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies
title_sort sequencing-based transcriptome-wide targeted genotyping for evolutionary and ecological studies
publisher SAGE Publishing
series Evolutionary Bioinformatics
issn 1176-9343
publishDate 2019-03-01
description Transcriptome-wide targeted genotyping is highly attractive for evolutionary and ecological studies but, until recently, accomplishing this goal presented a major technical barrier for the study of non-model organisms. Our group has recently developed a high-throughput targeted genotyping approach (called HD-Marker) based on the high specificity and accuracy of oligo extension-ligation assays that facilitates the design of assays tailored to meet specific genotyping needs. HD-Marker allows for targeted genotyping of over 10 000 genes in a single tube, with strikingly high capture rate (98%-99%) and genotyping accuracy (97%-99%). With the remarkable advantages of cost-effectiveness and flexibility, we envision that HD-Marker has broad application potential in evolutionary and ecological studies.
url https://doi.org/10.1177/1176934319836074
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AT jingwang sequencingbasedtranscriptomewidetargetedgenotypingforevolutionaryandecologicalstudies
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AT pingpingliu sequencingbasedtranscriptomewidetargetedgenotypingforevolutionaryandecologicalstudies
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