Cargando…
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...
Autores principales: | , , , , , , , , , |
---|---|
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 |
_version_ | 1784912030669471744 |
---|---|
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. |
format | Online Article Text |
id | pubmed-10038202 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | GigaScience Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT rameshbalan improvementstothegulfpipefishsyngnathusscovelligenome AT smallclaym improvementstothegulfpipefishsyngnathusscovelligenome AT healeyhope improvementstothegulfpipefishsyngnathusscovelligenome AT johnsonbernadette improvementstothegulfpipefishsyngnathusscovelligenome AT barkerelyse improvementstothegulfpipefishsyngnathusscovelligenome AT curreymark improvementstothegulfpipefishsyngnathusscovelligenome AT basshamsusan improvementstothegulfpipefishsyngnathusscovelligenome AT myersmegean improvementstothegulfpipefishsyngnathusscovelligenome AT creskowilliama improvementstothegulfpipefishsyngnathusscovelligenome AT jonesadamgregory improvementstothegulfpipefishsyngnathusscovelligenome |