Genetic diversity and temporal changes of an endemic cyprinid fish species, &lt;em&gt;Ancherythroculter nigrocauda&lt;/em&gt;, from the upper reaches of Yangtze River

Zhai, Dongdong; Li, Wenjing; Liu, Huanzhang; Cao, Weiguo; Gao, Xin

doi:10.24272/j.issn.2095-8137.2019.027

Cited by 14 publications

(7 citation statements)

References 35 publications

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“…Actually, aquaculture activities in the Tarim river basin are less developed due to the special environment (high salinity and sediment concentration) [ 33 , 34 ], and the natural populations of T. yarkandensis were actually less interfered by agricultural activities. In this context, although anthropogenic factors could affect the genetic structure and differentiation of fish populations [ 35 , 36 ], especially in some economic fish species widely cultured in aquaculture [ 14 , 37 ], we noted that the genetic exchange among most populations mediated by anthropogenic factors was limited in the Tarim River basin. Here, we suggest that the T. yarkandensis populations should be monitored in the long term to avoid significant reductions in abundance due to the genetic characterizations, including the high levels of genetic variation originating from among-population variation and the small effective population size.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Zhou

Zhao

et al. 2021

Biology

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The distribution of Triplophysa yarkandensis is restricted to Xinjiang’s Tarim River basin. We collected 119 T. yarkandensis samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a total of 164.81 Gb bases were generated with the Illumina platform, and 129,873 candidate SNPs were obtained with the Stacks pipeline for population genetic analyses. High levels of genetic diversity were detected among nine populations. The AMOVA results showed that the majority of genetic variations originated from among populations (FST = 0.67), and the pairwise FST values ranged from 0.4579 to 0.8736, indicating high levels of genetic differentiation among these populations. The discriminate analysis of principal components (DAPCs) and neighbor joining (NJ) tree revealed that the nine populations could be separated into two clusters (i.e., south and north populations), and modest genetic differentiation between south and north populations was observed, while the individuals from several populations were not clustered together by geographical location. The evidence of two genetic boundaries between south and north populations (except TTM) was supported by barrier analysis. The Bayesian skyline plotting indicated that T. yarkandensis populations in the Tarim River basin had not experienced genetic bottlenecks, and the effective population size remained stable. This study first clarified the genetic diversity and differentiation of T. yarkandensis populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.

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Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Zhou

Zhao

et al. 2021

Biology

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“…Ancherythroculter nigrocauda is a member of the subfamily Culterinae and it is one of the five currently recognized species of the genus Ancherythroculter (Froese & Pauly, 2019). Its distribution is restricted to the upper reaches of the Yangtze River (Liu, Zhu, Wang, & Tan, 2005) and it is an important commercial and aquaculture species in China (Zhai, Li, Liu, Cao, & Gao, 2019). In recent decades, A. nigrocauda has been used in artificial hybridization to generate hybrids with desirable traits, such as Pioneer No.…”

Section: Introductionmentioning

confidence: 99%

“…However, natural populations of A. nigrocauda have become threatened due to overfishing, dam construction and water pollution (Liu, 2013). Previous studies have focused mainly on genetic diversity (Liu et al, 2005; Zhai et al, 2019), reproductive biology (Liu et al, 2013), age and growth (Xue & He, 2001), oxygen‐resistance (Cao, Deng, & Wan, 2010; Li et al, 2017) and artificial propagation (Tan, Wang, Yan, & Dan, 2004; Yin & Lv, 2010). However, in‐depth analysis of A. nigrocauda biology and breeding is difficult because of a lack of genome resources.…”

Section: Introductionmentioning

confidence: 99%

High‐quality genome assembly and transcriptome of Ancherythroculter nigrocauda, an endemic Chinese cyprinid species

Zhang

Wang

et al. 2020

Molecular Ecology Resources

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Ancherythroculter nigrocauda is a cyprinid fish endemic of the upper reaches of the Yangtze River in China, where it is an important aquaculture and commercial species. It is also a threatened species as a result of overfishing, dam construction and water pollution. In this study, a chromosome-level genome assembly of A. nigrocauda is reported and built using PacBio sequencing and the Hi-C technology. The 1.04-Gb sequenced genome of A. nigrocauda contained 2,403 contigs, with an N50 length of 3.12 Mb. Then, 1,297 contigs, which represented 54.0% of all contigs and 97.2% of the whole content of the genome nucleotide base, were assembled into 24 chromosomes. Combined with transcriptome data from 10 tissues, 27,042 (78.5%) genes were functionally annotated out of 34,414 predicted protein-coding genes. Interestingly, high expression of many positively selected genes and expanded gene families in the brain suggested that these genes might play important roles in brain development in A. nigrocauda. Finally, we found tissue-specific expression of 10,732 genes. Functional analyses showed that they were mainly composed of genes related to (a) environmental information processing, (b) the circulatory system, and (c) development, suggesting they might be important for adaptation to different environments and for development of A. nigrocauda. The high-quality genome obtained in this study not only provides a valuable genomic resource for future studies of A. nigrocauda populations and conservation, but is also an important resource for further functional genomics studies of fishes.

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“…Thus, a better understanding of the indigenous sheep genetic diversity can pave way for devising conservation strategies; facilitate their effective use for future breeding programs and, formulating management policies. Genetic diversity is often assessed by molecular markers, including the nuclear microsatellites, also referred to as the simple sequence repeat markers (nSSR) and mitochondrial DNA (mtDNA) 9 . Nuclear SSR has been widely accepted as a useful tool for measuring genetic diversity and divergence within and among livestock populations 10 .…”

mentioning

confidence: 99%

Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India

Sharma

Ahlawat

Sharma

et al. 2020

Sci Rep

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Sheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.

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Genetic diversity and temporal changes of an endemic cyprinid fish species, <em>Ancherythroculter nigrocauda</em>, from the upper reaches of Yangtze River

Cited by 14 publications

References 35 publications

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

High‐quality genome assembly and transcriptome of Ancherythroculter nigrocauda, an endemic Chinese cyprinid species

Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India

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