Genetic and genomic architecture in eight strains of the laboratory opossum Monodelphis domestica.
Genetic and genomic architecture in eight strains of the laboratory opossum Monodelphis domestica.
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DOI：
10.1093/g3journal/jkab389
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发表时间：
2022-01-04
期刊：
影响因子：
--
通讯作者：
Wang X
中科院分区：
文献类型：
--
作者：
Xiong X;Samollow PB;Cao W;Metz R;Zhang C;Leandro AC;VandeBerg JL;Wang X
灰色短尾负鼠（Monodelphis arctica）是一种用于生物医学研究的实验室饲养的有袋动物模型。它是比较基因组学研究的关键物种，为真兽目哺乳动物谱系的基因组/表观基因组特征的衍生与祖先状态的研究提供了关键的系统发育外群。为了描述这种实验室有袋动物的当前遗传特征，我们检查了来自8个已建立的实验室菌株的79个个体。双酶切位点相关的DNA测序和全基因组重测序实验进行调查，在这些菌株的遗传结构。共鉴定了66，640个高质量的单核苷酸多态性（SNP）。我们分析了SNP密度，平均杂合性，核苷酸多样性，和人口分化参数Fst内和之间的八个菌株。主成分和群体结构分析清楚地解决了在其祖先的创始人群体的水平上的菌株，这些菌株的遗传结构正确地反映了他们的育种历史。我们证实了第一个近交实验室负鼠品系LSD（近交系数F > 0.99）和一个近近交品系FD 2 M1（0.98 < F < 0.99）的成功建立，这两个品系都来自不同的祖先背景。这些菌株适用于需要受控遗传背景的各种实验方案，以及可以产生具有信息性SNP的后代的杂交和回交，用于研究各种遗传和表观遗传过程。再加上最近在繁殖操作和CRISPR/Cas9技术方面的进展，独特的近交系的存在将使基因组编辑能够在不同的遗传背景下进行，极大地扩展了这种有袋动物模型在生物医学研究中的实用性。
The gray short-tailed opossum (Monodelphis domestica) is an established laboratory-bred marsupial model for biomedical research. It is a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs ancestral states of genomic/epigenomic characteristics for eutherian mammal lineages. To characterize the current genetic profile of this laboratory marsupial, we examined 79 individuals from eight established laboratory strains. Double digest restriction site-associated DNA sequencing and whole-genome resequencing experiments were performed to investigate the genetic architecture in these strains. A total of 66,640 high-quality single nucleotide polymorphisms (SNPs) were identified. We analyzed SNP density, average heterozygosity, nucleotide diversity, and population differentiation parameter Fst within and between the eight strains. Principal component and population structure analysis clearly resolve the strains at the level of their ancestral founder populations, and the genetic architecture of these strains correctly reflects their breeding history. We confirmed the successful establishment of the first inbred laboratory opossum strain LSD (inbreeding coefficient F > 0.99) and a nearly inbred strain FD2M1 (0.98 < F < 0.99), each derived from a different ancestral background. These strains are suitable for various experimental protocols requiring controlled genetic backgrounds and for intercrosses and backcrosses that can generate offspring with informative SNPs for studying a variety of genetic and epigenetic processes. Together with recent advances in reproductive manipulation and CRISPR/Cas9 techniques for Monodelphis domestica, the existence of distinctive inbred strains will enable genome editing on different genetic backgrounds, greatly expanding the utility of this marsupial model for biomedical research.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
1.5
作者：
Hornecker, Jacey L.;Samollow, Paul B.;McCarrey, John R.
通讯作者：
McCarrey, John R.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
3
作者：
Alexander DH;Lange K
通讯作者：
Lange K
影响因子：
4.4
作者：
Das, Radhika;Anderson, Nathan;Jirtle, Randy L.
通讯作者：
Jirtle, Randy L.