Cargando…

The reference genome assembly of the bright cobblestone lichen, Acarospora socialis

Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been con...

Descripción completa

Detalles Bibliográficos
Autores principales: Adams, Julia N, Escalona, Merly, Marimuthu, Mohan P A, Fairbairn, Colin W, Beraut, Eric, Seligmann, William, Nguyen, Oanh, Chumchim, Noravit, Stajich, Jason E
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10650946/
https://www.ncbi.nlm.nih.gov/pubmed/37740386
http://dx.doi.org/10.1093/jhered/esad052
_version_ 1785135898075070464
author Adams, Julia N
Escalona, Merly
Marimuthu, Mohan P A
Fairbairn, Colin W
Beraut, Eric
Seligmann, William
Nguyen, Oanh
Chumchim, Noravit
Stajich, Jason E
author_facet Adams, Julia N
Escalona, Merly
Marimuthu, Mohan P A
Fairbairn, Colin W
Beraut, Eric
Seligmann, William
Nguyen, Oanh
Chumchim, Noravit
Stajich, Jason E
author_sort Adams, Julia N
collection PubMed
description Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.
format Online
Article
Text
id pubmed-10650946
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-106509462023-09-07 The reference genome assembly of the bright cobblestone lichen, Acarospora socialis Adams, Julia N Escalona, Merly Marimuthu, Mohan P A Fairbairn, Colin W Beraut, Eric Seligmann, William Nguyen, Oanh Chumchim, Noravit Stajich, Jason E J Hered Genome Resources Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California. Oxford University Press 2023-09-07 /pmc/articles/PMC10650946/ /pubmed/37740386 http://dx.doi.org/10.1093/jhered/esad052 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
Adams, Julia N
Escalona, Merly
Marimuthu, Mohan P A
Fairbairn, Colin W
Beraut, Eric
Seligmann, William
Nguyen, Oanh
Chumchim, Noravit
Stajich, Jason E
The reference genome assembly of the bright cobblestone lichen, Acarospora socialis
title The reference genome assembly of the bright cobblestone lichen, Acarospora socialis
title_full The reference genome assembly of the bright cobblestone lichen, Acarospora socialis
title_fullStr The reference genome assembly of the bright cobblestone lichen, Acarospora socialis
title_full_unstemmed The reference genome assembly of the bright cobblestone lichen, Acarospora socialis
title_short The reference genome assembly of the bright cobblestone lichen, Acarospora socialis
title_sort reference genome assembly of the bright cobblestone lichen, acarospora socialis
topic Genome Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10650946/
https://www.ncbi.nlm.nih.gov/pubmed/37740386
http://dx.doi.org/10.1093/jhered/esad052
work_keys_str_mv AT adamsjulian thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT escalonamerly thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT marimuthumohanpa thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT fairbairncolinw thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT berauteric thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT seligmannwilliam thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT nguyenoanh thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT chumchimnoravit thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT stajichjasone thereferencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT adamsjulian referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT escalonamerly referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT marimuthumohanpa referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT fairbairncolinw referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT berauteric referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT seligmannwilliam referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT nguyenoanh referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT chumchimnoravit referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis
AT stajichjasone referencegenomeassemblyofthebrightcobblestonelichenacarosporasocialis