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来自鳉属(鳉科,鲤齿目)三个物种的全基因组序列。

The Complete Genome Sequences of three species from the killifish genus (Rivulidae, Cyprinodontiformes).

作者信息

Berbel-Filho Waldir M, Pirro Stacy, Thompson Andrew W, Lima Sergio M Q, Consuegra Sofia, Betancur Ricardo

机构信息

Department of Biology, University of Oklahoma.

Biodiversity, Iridian Genomes.

出版信息

Biodivers Genomes. 2023;2023. doi: 10.56179/001c.77448. Epub 2023 May 24.

DOI:10.56179/001c.77448
PMID:37483464
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10361417/
Abstract

The killifish genus currently contains seven recognized species found in freshwater and mangrove microhabitats in South and Central America, the Caribbean, and Florida. species have several unique features. Beyond its amphibious nature, two of the species ( and Costa 2011) are the only known vertebrates capable of self-fertilization. Although reference genomes for self-fertilizing species are readily available, a complete understanding of the genomic basis leading to the transition in mating systems in the genus requires more genomic resources at a broader taxonomic level. Here, we present the complete genome sequences for three species from Brazil: the endangered freshwater species and and the androdiecious but obligate outcrossing ( Costa 2011). The raw data and assembled genomes are available in GenBank.

摘要

鳉鱼属目前包含七个已确认的物种,分布于南美洲、中美洲、加勒比地区和佛罗里达州的淡水和红树林微生境中。这些物种具有几个独特的特征。除了其两栖特性外,其中两个物种(Costa 2011)是已知仅有的能够自我受精的脊椎动物。尽管自我受精物种的参考基因组很容易获得,但要全面了解导致该属交配系统转变的基因组基础,还需要在更广泛的分类水平上有更多的基因组资源。在这里,我们展示了来自巴西的三个鳉鱼物种的完整基因组序列:濒危淡水物种和以及雌雄同体但 obligate outcrossing(Costa 2011)。原始数据和组装好的基因组可在GenBank中获取。 (注:原文中“androdiecious but obligate outcrossing”这里“obligate outcrossing”可能有误,不太明确准确意思,按原文翻译了)

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本文引用的文献

1
Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias.系统基因组学揭示了脂鲤科的小鱵属中的广泛基因渗入和一个线粒体-核不符的案例。
Mol Phylogenet Evol. 2022 Dec;177:107617. doi: 10.1016/j.ympev.2022.107617. Epub 2022 Aug 28.
2
More than Breathing Air: Evolutionary Drivers and Physiological Implications of an Amphibious Lifestyle in Fishes.超越呼吸空气:鱼类两栖生活方式的进化驱动力和生理意义。
Physiology (Bethesda). 2021 Sep 1;36(5):307-314. doi: 10.1152/physiol.00012.2021.
3
More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast.
所见不止所现:在巴西沿海,同域分布且形态相似的红树林马鲅具有不同的交配系统和遗传结构模式。
Heredity (Edinb). 2020 Nov;125(5):340-352. doi: 10.1038/s41437-020-00356-y. Epub 2020 Aug 21.
4
Trimmomatic: a flexible trimmer for Illumina sequence data.Trimmomatic:一款适用于 Illumina 测序数据的灵活修剪工具。
Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1.
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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.SPAdes:一种新的基因组组装算法及其在单细胞测序中的应用
J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16.
6
Long-term retention of self-fertilization in a fish clade.一个鱼类分支中自体受精的长期保留
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14456-9. doi: 10.1073/pnas.0907852106. Epub 2009 Aug 17.
7
Phylogeny of the Neotropical killifish family Rivulidae (Cyprinodontiformes, Aplocheiloidei) inferred from mitochondrial DNA sequences.基于线粒体DNA序列推断新热带鳉科(鲤齿目,溪鳉亚目)的系统发育
Mol Phylogenet Evol. 1999 Nov;13(2):289-301. doi: 10.1006/mpev.1999.0656.