基因组时代的博物馆收藏重访:MIG-seq在从蚂蚁(膜翅目:蚁科)和其他小生物的古老微小干燥标本中检索系统发育信息的潜力

IF 3.8 1区 农林科学 Q1 ENTOMOLOGY
K. Eguchi, Emiko Oguri, Takanori Sasaki, A. Matsuo, D. Nguyen, W. Jaitrong, B. E. Yahya, Zhilin Chen, R. Satria, Wendy Y. Wang, Y. Suyama
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引用次数: 8

摘要

通过测序进行多重简单序列重复基因分型- MIG-seq -是使用下一代测序平台进行全基因组SNP检测的一种有效的基于pcr的方法,它为博物馆组学的一个核心问题提供了潜在的解决方案-从老化标本中获得有用的序列数据的困难,这些标本通常降解和/或低产量的DNA。我们演示并验证了MIG-seq工作流程在从古老的博物馆标本中获得有用和稳健的序列数据方面的成本效益和效用。我们采用MIG-seq方法对55个年龄(10 23岁)毫米大小的高度多样化蚁属Pheidole干装标本进行了分析。55个样本共生成了50,782,736个reads(每个样本259,902 3,693,375个reads)。这些reads对应4849个多态性位点的36862个snp;然后使用SNP数据集构建贝叶斯系统发育树。系统发育树的拓扑结构与现存的斐多乐种间系统发育关系的知识高度一致。因此,我们推荐MIG-seq方法作为一种成本效益高且高度适用的管道,用于对老年博物馆标本进行系统发育和群体遗传研究,潜在地增强标本库与现代生物多样性科学和保护生物学的相关性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Revisiting museum collections in the genomic era: potential of MIG-seq for retrieving phylogenetic information from aged minute dry specimens of ants (Hymenoptera: Formicidae) and other small organisms
Multiplexed inter-simple sequence repeat genotyping by sequencing – MIG-seq – is an effective PCR-based method for genome-wide SNP detection using the Next-Generation Sequencing platform, and it provides a potential solution to a central problem in museomics – the difficulties of obtaining useful sequence data from aged specimens with often degraded and / or low yields of DNA. We demonstrate and validate the cost effectiveness and utility of the MIG-seq workflow in obtaining useful and robust sequence data from aged museum specimens. We applied the MIG-seq approach to 55 aged (10 23 years old) millimeter-sized dry-mounted specimens of the hyper-diverse ant genus Pheidole. A total of 50,782,736 reads were generated from the 55 samples (259,902 3,693,375 reads per sample). The reads corresponded to 36,862 SNPs from 4,849 polymorphic loci; the SNP dataset was then used to construct a Bayesian phylogenetic tree. The topology of the phylogenetic tree was highly compatible with existing knowledge of phylogenetic relationships among species of Pheidole. Therefore, we recommend the MIG-seq method as a cost-effective and highly applicable pipeline for conducting phylogenetic and population genetic studies on aged museum specimens, potentially enhancing the relevance of specimen repositories in general towards modern biodiversity science and conservation biology.
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来源期刊
Myrmecological News
Myrmecological News ENTOMOLOGY-
CiteScore
7.30
自引率
4.90%
发文量
0
审稿时长
>12 weeks
期刊介绍: Taxonomic manuscripts with isolated species descriptions are generally discouraged, especially for genera with large numbers of undescribed species; it lies at the discretion of the editorial team whether such manuscripts are considered. Papers on new distribution records will be considered if the new records are sufficiently important or unexpected from a biogeographical perspective. Such papers could, for example, discuss relevant biological/ecological data and/or biogeographical implications such as analysis by species-distribution modelling. In detail, research areas covered by Myrmecological News include: behaviour; biogeography and faunistics; biological-pest control; chemical ecology; climate-change biology; cognition and learning; comparative and functional morphology; community ecology; conservation biology and bioindication; cytogenetics; ecology and evolution of (endo)symbioses; ecosystem (dis)services; foraging strategies; fossils; fragmentation ecology; genomics; histology; immune research; (integrative) taxonomy; interspecific hybridisation; invasion biology; life-history research; methodology in community quantification; national checklists; neurobiology; niche ecology; orientation and navigation; phenology; phylogeny and phylogeography; population genetics; sensory physiology; social evolution; social parasitism; sociogenomics; stable isotopes; tools for routine identification.
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