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Reference genome of the Virginia rail, Rallus limicola

The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with gener...

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Autores principales: Hall, Laurie A, Wang, Ian J, Escalona, Merly, Beraut, Eric, Sacco, Samuel, Sahasrabudhe, Ruta, Nguyen, Oanh, Toffelmier, Erin, Shaffer, H Bradley, Beissinger, Steven R
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10287147/
https://www.ncbi.nlm.nih.gov/pubmed/37105531
http://dx.doi.org/10.1093/jhered/esad026
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author Hall, Laurie A
Wang, Ian J
Escalona, Merly
Beraut, Eric
Sacco, Samuel
Sahasrabudhe, Ruta
Nguyen, Oanh
Toffelmier, Erin
Shaffer, H Bradley
Beissinger, Steven R
author_facet Hall, Laurie A
Wang, Ian J
Escalona, Merly
Beraut, Eric
Sacco, Samuel
Sahasrabudhe, Ruta
Nguyen, Oanh
Toffelmier, Erin
Shaffer, H Bradley
Beissinger, Steven R
author_sort Hall, Laurie A
collection PubMed
description The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.
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spelling pubmed-102871472023-06-23 Reference genome of the Virginia rail, Rallus limicola Hall, Laurie A Wang, Ian J Escalona, Merly Beraut, Eric Sacco, Samuel Sahasrabudhe, Ruta Nguyen, Oanh Toffelmier, Erin Shaffer, H Bradley Beissinger, Steven R J Hered Genome Resources The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes. Oxford University Press 2023-04-27 /pmc/articles/PMC10287147/ /pubmed/37105531 http://dx.doi.org/10.1093/jhered/esad026 Text en © The American Genetic Association. 2023. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Genome Resources
Hall, Laurie A
Wang, Ian J
Escalona, Merly
Beraut, Eric
Sacco, Samuel
Sahasrabudhe, Ruta
Nguyen, Oanh
Toffelmier, Erin
Shaffer, H Bradley
Beissinger, Steven R
Reference genome of the Virginia rail, Rallus limicola
title Reference genome of the Virginia rail, Rallus limicola
title_full Reference genome of the Virginia rail, Rallus limicola
title_fullStr Reference genome of the Virginia rail, Rallus limicola
title_full_unstemmed Reference genome of the Virginia rail, Rallus limicola
title_short Reference genome of the Virginia rail, Rallus limicola
title_sort reference genome of the virginia rail, rallus limicola
topic Genome Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10287147/
https://www.ncbi.nlm.nih.gov/pubmed/37105531
http://dx.doi.org/10.1093/jhered/esad026
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