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Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)

Tamias sibiricus is regarded as one predominant scatter-hoarder that stores their food items both in small scattered caches and underground larder-hoards. This unique behavior, though providing essential seed dispersal services for many plant species worldwide, relies highly on accurate spatial memo...

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Autores principales: Li, Ran, Zhang, Mingfei, Cha, Muha, Xiang, Jishan, Yi, Xianfeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9790022/
https://www.ncbi.nlm.nih.gov/pubmed/36566231
http://dx.doi.org/10.1038/s41597-022-01910-5
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author Li, Ran
Zhang, Mingfei
Cha, Muha
Xiang, Jishan
Yi, Xianfeng
author_facet Li, Ran
Zhang, Mingfei
Cha, Muha
Xiang, Jishan
Yi, Xianfeng
author_sort Li, Ran
collection PubMed
description Tamias sibiricus is regarded as one predominant scatter-hoarder that stores their food items both in small scattered caches and underground larder-hoards. This unique behavior, though providing essential seed dispersal services for many plant species worldwide, relies highly on accurate spatial memory and acute sense of olfaction. Here, we assembled a chromosome-scale genome of T. sibiricus using Illumina sequencing, PacBio sequencing and chromosome structure capture technique. The genome was 2.64 Gb in size with scaffold N50 length of 172.61 Mb. A total of 2.59 Gb genome data was anchored and orientated onto 19 chromosomes (ranging from 28.70 to 222.90 Mb) with a mounting rate of up to 98.03%. Meanwhile, 25,311 protein-coding genes were predicted with an average gene length of 32,936 bp, and 94.73% of these genes were functionally annotated. This reference genome will be a valuable resource for in-depth studies on basic biological possess and environmental adaptation of the Siberian chipmunk, as well as promoting comparative genomic analyses with other species within Rodentia.
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spelling pubmed-97900222022-12-26 Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus) Li, Ran Zhang, Mingfei Cha, Muha Xiang, Jishan Yi, Xianfeng Sci Data Data Descriptor Tamias sibiricus is regarded as one predominant scatter-hoarder that stores their food items both in small scattered caches and underground larder-hoards. This unique behavior, though providing essential seed dispersal services for many plant species worldwide, relies highly on accurate spatial memory and acute sense of olfaction. Here, we assembled a chromosome-scale genome of T. sibiricus using Illumina sequencing, PacBio sequencing and chromosome structure capture technique. The genome was 2.64 Gb in size with scaffold N50 length of 172.61 Mb. A total of 2.59 Gb genome data was anchored and orientated onto 19 chromosomes (ranging from 28.70 to 222.90 Mb) with a mounting rate of up to 98.03%. Meanwhile, 25,311 protein-coding genes were predicted with an average gene length of 32,936 bp, and 94.73% of these genes were functionally annotated. This reference genome will be a valuable resource for in-depth studies on basic biological possess and environmental adaptation of the Siberian chipmunk, as well as promoting comparative genomic analyses with other species within Rodentia. Nature Publishing Group UK 2022-12-24 /pmc/articles/PMC9790022/ /pubmed/36566231 http://dx.doi.org/10.1038/s41597-022-01910-5 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Data Descriptor
Li, Ran
Zhang, Mingfei
Cha, Muha
Xiang, Jishan
Yi, Xianfeng
Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)
title Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)
title_full Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)
title_fullStr Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)
title_full_unstemmed Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)
title_short Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)
title_sort chromosome-level genome assembly of the siberian chipmunk (tamias sibiricus)
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9790022/
https://www.ncbi.nlm.nih.gov/pubmed/36566231
http://dx.doi.org/10.1038/s41597-022-01910-5
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