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在斑点叉尾鮰基因组中重复元件的注释。

The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus).

机构信息

School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America.

USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, Mississippi, United States of America.

出版信息

PLoS One. 2018 May 15;13(5):e0197371. doi: 10.1371/journal.pone.0197371. eCollection 2018.

DOI:10.1371/journal.pone.0197371
PMID:29763462
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5953449/
Abstract

Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalence of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions.

摘要

斑点叉尾鮰（Ictalurus punctatus）是一种高度适应环境的物种，已被用作比较免疫学、生理学和冷血脊椎动物毒理学的研究模型。它在水产养殖中也具有重要的经济价值。因此，其参考基因组已经生成并注释了蛋白质编码基因。然而，鮰鱼基因组中的重复元件还不太清楚。在这项研究中，在斑点叉尾鮰基因组中鉴定和表征了超过 417.8 兆碱基（MB）的重复元件。其中，DNA/TcMar-Tc1 转座子是最丰富的类型，约占总重复元件的 20%，其次是微卫星（14%）。重复元件的普遍性，尤其是移动元件，可能为鮰鱼基因组的进化提供了动力。鉴定出了一些鮰鱼特有的重复元件，包括先前报道的 Xba 元件，其分化率相对较低，比基因的非翻译区慢，但比蛋白质编码序列快，表明其进化受到限制。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/6ccbab00e1b2/pone.0197371.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/028e6eeb970f/pone.0197371.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/0808ef66b1b3/pone.0197371.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/cb9168e3f9b1/pone.0197371.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/eb49848349be/pone.0197371.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/6ccbab00e1b2/pone.0197371.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/028e6eeb970f/pone.0197371.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/0808ef66b1b3/pone.0197371.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/cb9168e3f9b1/pone.0197371.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/eb49848349be/pone.0197371.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7b3/5953449/6ccbab00e1b2/pone.0197371.g005.jpg

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