Characterization of novel microsatellite markers of the Emei Shan Liocichla using restriction site-associated DNA sequencing

Yang, Ailin; Chen, De; Wang, Pengcheng; Fu, Yiqiang; Zhang, Zhengwang

doi:10.1186/s40657-017-0071-8

Cited by 7 publications

(6 citation statements)

References 42 publications

(43 reference statements)

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“…Since the total length of SSR markers is generally short, the development of SSRs does not require a high‐quality reference genome. Previous studies usually used sequence reads from the sequenced individual to assembly a draft genome to mine SSR sequences (Koshiishi et al, 2021; Yang et al, 2017). As for the multi‐sample strategy, we used multi‐sample low‐depth data to generate a draft reference genome inspired by pan‐genome strategies, The scaffold and contig N50 of the assembled genome were approximately 134 kb and 100 kb, respectively, which are lower than those of the canonical high‐quality genome (scaffold/contig N50: 3,632.75 kb/112.76 kb; Wang et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

Wang

Gao

Liu

et al. 2022

Ecology and Evolution

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Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.

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Section: Discussionmentioning

confidence: 99%

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

Wang

Gao

Liu

et al. 2022

Ecology and Evolution

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“…Because of their relatively high level of polymorphism, repeatability in genotyping and high PCR amplification success, microsatellites are advantageous genetic tool to address conservation and behavioural genetic patterns in threatened species towards their conservation and management issues ( Faria et al, 2016 ; Wang et al, 2017 ). A key part of microsatellite-based conservation genetics is to develop either species-specific or cross-species primer sets, with the development of next-generation sequencing, the development of reliable microsatellites are no longer an time-consuming task, even for birds that have few known microsatellite loci in their genomes ( Castoe et al, 2012 ; Wang et al, 2017 ; Yang et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites

Chen

Zheng²,

Wan

et al. 2019

PeerJ

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Background Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate. Results Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the probability that the origin of the Hong Kong captive population was the wild population from Wuyuan. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.

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“…Because of their relatively high level of polymorphism, repeatability in genotyping and high PCR amplification success, microsatellites are advantageous genetic tool to address conservation and behavioural genetic patterns in threatened species towards their conservation and management issues (Faria et al, 2016;Wang et al, 2017). A key part of microsatellite-based conservation genetics is to develop either species-specific or cross-species primer sets, with the development of next-generation sequencing, the development of reliable microsatellites are no longer an timeconsuming task, even for birds that have few known microsatellite loci in their genomes (Castoe et al, 2012;Wang et al, 2017;Yang et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites (v0.2)"

2019

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Background. Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Bluecrowned Laughingthrush , Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China.We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods. Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010-2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences.Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate. Results. Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion. This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the probability that the origin of the Hong Kong captive population was the wild population from Wuyuan. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.

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Characterization of novel microsatellite markers of the Emei Shan Liocichla using restriction site-associated DNA sequencing

Cited by 7 publications

References 42 publications

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites

Peer Review #1 of "Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites (v0.2)"

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