Conservation Genetics Resources最新文献

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Development of SSR markers in top-mouth culter (Erythroculter ilishaeformis) based on high-throughput sequencing 基于高通量测序的上口菌SSR标记的开发

IF 1.1 4区环境科学与生态学 Q3 Agricultural and Biological Sciences

Conservation Genetics Resources

Pub Date : 2023-11-16 DOI: 10.1007/s12686-023-01336-0

Huimin Xu, Bing Gong, Dandan Ju, Mingsong Xiao

The top-mouth culter Erythroculter ilishaeformis is a kind of carnivorous fish that is currently a widely distributed fish in China, which is a commercially important freshwater fish in China. However, only few effective molecular markers on E. ilishaeformis are available. In this study, nine muscles and liver tissues of cDNA libraries of E. ilishaeformis were sequenced using Illumina HiSeq4000 paired-end sequencing technology. 86,574 sequences from 80,945,107 paired-end reads were generated. 55 novel simple sequence repeat (SSR) markers were developed based on high-throughput sequencing. After genetic diversity analysis, observed heterozygosity (Ho) was from 0.1613 to 0.4839. Expected heterozygosity (He) was from 0.1507 to 0.3728. Minor allele frequencies (MAFs) were from 0.3333 to 0.5000, and Hardy-Weinberg values were relatively balanced. These SSR markers developed from transcriptome sequencing will be as a useful tool to exploit populations genetic of E. ilishaeformis.

上嘴鱼(Erythroculter ilishaeformis)是一种肉食性鱼类，是目前中国广泛分布的鱼类，是中国重要的商业淡水鱼。然而，目前对伊利沙氏芽孢杆菌有效的分子标记很少。本研究采用Illumina HiSeq4000对端测序技术，对伊氏拟鳗cDNA文库中的9个肌肉和肝脏组织进行了测序。从80,945,107对末端reads中产生86,574个序列。利用高通量测序技术，开发了55个新的SSR标记。经遗传多样性分析，观察到的杂合度(Ho)为0.1613 ~ 0.4839。期望杂合度(He)在0.1507 ~ 0.3728之间。次要等位基因频率(MAFs)在0.3333 ~ 0.5000之间，Hardy-Weinberg值相对平衡。通过转录组测序开发出的SSR标记将为利用伊氏拟虫群体遗传资源提供有用的工具。

引用次数: 0

An R-based tool for identifying sex-linked markers from restriction site-associated DNA sequencing with applications to elasmobranch conservation 一个基于r的工具，用于从限制性位点相关DNA测序中识别性别连锁标记，并应用于elasmobranch保护

IF 1.1 4区环境科学与生态学 Q3 Agricultural and Biological Sciences

Conservation Genetics Resources

Pub Date : 2023-11-16 DOI: 10.1007/s12686-023-01331-5

Floriaan Devloo-Delva, Thierry Gosselin, Paul A. Butcher, Peter M. Grewe, Charlie Huveneers, Robin B. Thomson, Jonathan M. Werry, Pierre Feutry

Identifying sex-linked markers from genomic data has both theoretical and applied importance, especially in conservation. Yet, few methods and tools exist to detect such markers from Restriction-site-Associated DNA sequencing reads and even fewer tools can identify sex-linked markers from existing genotyped data. Here, we describe a new R function that can identify sex-linked markers in species with partially non-recombining sex chromosomes. We test the accuracy and speed of our function with an example dataset from a species of conservation concern, the White Shark, Carcharodon carcharias. We further compare our method against other approaches and find that our method detects more sex-linked markers that can be reliably mapped to reference genomes. Overall, we provide a conservation and fisheries-relevant tool that can reliably and efficiently assign sex from genetic data in species with a heterogametic sex and we demonstrate its utility by developing a sex-identification PCR test for White Sharks.

从基因组数据中识别性别连锁标记具有理论和应用意义，特别是在保护方面。然而，很少有方法和工具可以从限制性位点相关的DNA测序读数中检测这些标记，甚至更少的工具可以从现有的基因分型数据中识别性别连锁标记。在这里，我们描述了一个新的R函数，可以识别部分不重组性染色体的物种的性别连锁标记。我们用一个样本数据集来测试我们的函数的准确性和速度，这个样本数据集来自一个受保护的物种，白鲨，Carcharodon carcharias。我们进一步将我们的方法与其他方法进行比较，发现我们的方法可以检测到更多的性别连锁标记，这些标记可以可靠地映射到参考基因组。总的来说，我们提供了一个保护和渔业相关的工具，可以可靠和有效地从具有异配子性别的物种的遗传数据中确定性别，我们通过开发白鲨性别鉴定PCR测试来证明它的实用性。

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引用次数: 2

Multiplex PCR assay to distinguish among three widespread brown frog species 三种分布广泛的褐蛙的多重PCR鉴别