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Improvements to the Gulf pipefish Syngnathus scovelli genome

The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first S. s...

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Autores principales: Ramesh, Balan, Small, Clay M., Healey, Hope, Johnson, Bernadette, Barker, Elyse, Currey, Mark, Bassham, Susan, Myers, Megean, Cresko, William A., Jones, Adam Gregory
Formato: Online Artículo Texto
Lenguaje:English
Publicado: GigaScience Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10038202/
https://www.ncbi.nlm.nih.gov/pubmed/36969711
http://dx.doi.org/10.46471/gigabyte.76
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author Ramesh, Balan
Small, Clay M.
Healey, Hope
Johnson, Bernadette
Barker, Elyse
Currey, Mark
Bassham, Susan
Myers, Megean
Cresko, William A.
Jones, Adam Gregory
author_facet Ramesh, Balan
Small, Clay M.
Healey, Hope
Johnson, Bernadette
Barker, Elyse
Currey, Mark
Bassham, Susan
Myers, Megean
Cresko, William A.
Jones, Adam Gregory
author_sort Ramesh, Balan
collection PubMed
description The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first S. scovelli genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation. Here, using PacBio long-read high-fidelity sequences and a proximity ligation library, we generate an improved assembly to obtain 22 chromosome-level scaffolds. Compared to the first assembly, the gaps in the improved assembly are smaller, the N75 is larger, and our genome is ~95% BUSCO complete. Using a large body of RNA-Seq reads from different tissue types and NCBI's Eukaryotic Annotation Pipeline, we discovered 28,162 genes, of which 8,061 are non-coding genes. Our new genome assembly and annotation are tagged as a RefSeq genome by NCBI and provide enhanced resources for research work involving S. scovelli.
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spelling pubmed-100382022023-03-25 Improvements to the Gulf pipefish Syngnathus scovelli genome Ramesh, Balan Small, Clay M. Healey, Hope Johnson, Bernadette Barker, Elyse Currey, Mark Bassham, Susan Myers, Megean Cresko, William A. Jones, Adam Gregory GigaByte Data Release The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first S. scovelli genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation. Here, using PacBio long-read high-fidelity sequences and a proximity ligation library, we generate an improved assembly to obtain 22 chromosome-level scaffolds. Compared to the first assembly, the gaps in the improved assembly are smaller, the N75 is larger, and our genome is ~95% BUSCO complete. Using a large body of RNA-Seq reads from different tissue types and NCBI's Eukaryotic Annotation Pipeline, we discovered 28,162 genes, of which 8,061 are non-coding genes. Our new genome assembly and annotation are tagged as a RefSeq genome by NCBI and provide enhanced resources for research work involving S. scovelli. GigaScience Press 2023-02-20 /pmc/articles/PMC10038202/ /pubmed/36969711 http://dx.doi.org/10.46471/gigabyte.76 Text en © The Author(s) 2023. 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 Data Release
Ramesh, Balan
Small, Clay M.
Healey, Hope
Johnson, Bernadette
Barker, Elyse
Currey, Mark
Bassham, Susan
Myers, Megean
Cresko, William A.
Jones, Adam Gregory
Improvements to the Gulf pipefish Syngnathus scovelli genome
title Improvements to the Gulf pipefish Syngnathus scovelli genome
title_full Improvements to the Gulf pipefish Syngnathus scovelli genome
title_fullStr Improvements to the Gulf pipefish Syngnathus scovelli genome
title_full_unstemmed Improvements to the Gulf pipefish Syngnathus scovelli genome
title_short Improvements to the Gulf pipefish Syngnathus scovelli genome
title_sort improvements to the gulf pipefish syngnathus scovelli genome
topic Data Release
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10038202/
https://www.ncbi.nlm.nih.gov/pubmed/36969711
http://dx.doi.org/10.46471/gigabyte.76
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