Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing
Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these speci...
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doaj-2c64446c7d904f25a06c19b33fae0be22020-11-24T23:41:42ZengMDPI AGMolecules1420-30492016-01-012116710.3390/molecules21010067molecules21010067Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation SequencingChiuan-Yu Li0Tzen-Yuh Chiang1Yu-Chung Chiang2Hsin-Mei Hsu3Xue-Jun Ge4Chi-Chun Huang5Chaur-Tzuhn Chen6Kuo-Hsiang Hung7Taiwan Endemic Species Research Institute, Nantou 552, TaiwanDepartment of Life Sciences, National Cheng-Kung University, Tainan 701, TaiwanDepartment of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, TaiwanDepartment of Forestry, Pingtung University of Science and Technology, Pingtung 912, TaiwanSouth China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKinmen National Park, Kinmen 892, TaiwanDepartment of Forestry, Pingtung University of Science and Technology, Pingtung 912, TaiwanGraduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, TaiwanAmentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs) from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1–4, the polymorphism information content ranged from 0.000–0.692, and the observed and expected heterozygosity were 0.000–1.000 and 0.080–0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species.http://www.mdpi.com/1420-3049/21/1/67Amentotaxusendangered speciesEST-SSR markersgenetic diversitytranscriptome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Chiuan-Yu Li Tzen-Yuh Chiang Yu-Chung Chiang Hsin-Mei Hsu Xue-Jun Ge Chi-Chun Huang Chaur-Tzuhn Chen Kuo-Hsiang Hung |
spellingShingle |
Chiuan-Yu Li Tzen-Yuh Chiang Yu-Chung Chiang Hsin-Mei Hsu Xue-Jun Ge Chi-Chun Huang Chaur-Tzuhn Chen Kuo-Hsiang Hung Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing Molecules Amentotaxus endangered species EST-SSR markers genetic diversity transcriptome |
author_facet |
Chiuan-Yu Li Tzen-Yuh Chiang Yu-Chung Chiang Hsin-Mei Hsu Xue-Jun Ge Chi-Chun Huang Chaur-Tzuhn Chen Kuo-Hsiang Hung |
author_sort |
Chiuan-Yu Li |
title |
Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing |
title_short |
Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing |
title_full |
Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing |
title_fullStr |
Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing |
title_full_unstemmed |
Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing |
title_sort |
cross-species, amplifiable est-ssr markers for amentotaxus species obtained by next-generation sequencing |
publisher |
MDPI AG |
series |
Molecules |
issn |
1420-3049 |
publishDate |
2016-01-01 |
description |
Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs) from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1–4, the polymorphism information content ranged from 0.000–0.692, and the observed and expected heterozygosity were 0.000–1.000 and 0.080–0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species. |
topic |
Amentotaxus endangered species EST-SSR markers genetic diversity transcriptome |
url |
http://www.mdpi.com/1420-3049/21/1/67 |
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