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A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)

North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary...

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Autores principales: Ludt, William B, Corbett, Eamon C, Kattawar, Jerry, Chakrabarty, Prosanta, Faircloth, Brant C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997549/
https://www.ncbi.nlm.nih.gov/pubmed/36683458
http://dx.doi.org/10.1093/g3journal/jkad019
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author Ludt, William B
Corbett, Eamon C
Kattawar, Jerry
Chakrabarty, Prosanta
Faircloth, Brant C
author_facet Ludt, William B
Corbett, Eamon C
Kattawar, Jerry
Chakrabarty, Prosanta
Faircloth, Brant C
author_sort Ludt, William B
collection PubMed
description North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids.
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spelling pubmed-99975492023-03-10 A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus) Ludt, William B Corbett, Eamon C Kattawar, Jerry Chakrabarty, Prosanta Faircloth, Brant C G3 (Bethesda) Genome Report North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids. Oxford University Press 2023-01-23 /pmc/articles/PMC9997549/ /pubmed/36683458 http://dx.doi.org/10.1093/g3journal/jkad019 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Ludt, William B
Corbett, Eamon C
Kattawar, Jerry
Chakrabarty, Prosanta
Faircloth, Brant C
A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
title A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
title_full A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
title_fullStr A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
title_full_unstemmed A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
title_short A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
title_sort reference genome for bluegill (centrarchidae: lepomis macrochirus)
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997549/
https://www.ncbi.nlm.nih.gov/pubmed/36683458
http://dx.doi.org/10.1093/g3journal/jkad019
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