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Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz

Acacia tree population is declining in several countries of the world especially in the Arabian peninsula due to human-induced activities. The tree has potential medicinal and economic benefits as a source of fuel and timber. It can fix nitrogen, a significant property that assists in desert rehabil...

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Autores principales: Habibi, Nazima, Al Salameen, Fadila, Rahman, Muhammed, Kumar, Vinod, Al Amad, Sami, Shajan, Anisha, Zakir, Farhana, Abdul Razzack, Nasreem, Tinwala, Waiel Hussain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8933827/
https://www.ncbi.nlm.nih.gov/pubmed/35313494
http://dx.doi.org/10.1016/j.dib.2022.108031
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author Habibi, Nazima
Al Salameen, Fadila
Rahman, Muhammed
Kumar, Vinod
Al Amad, Sami
Shajan, Anisha
Zakir, Farhana
Abdul Razzack, Nasreem
Tinwala, Waiel Hussain
author_facet Habibi, Nazima
Al Salameen, Fadila
Rahman, Muhammed
Kumar, Vinod
Al Amad, Sami
Shajan, Anisha
Zakir, Farhana
Abdul Razzack, Nasreem
Tinwala, Waiel Hussain
author_sort Habibi, Nazima
collection PubMed
description Acacia tree population is declining in several countries of the world especially in the Arabian peninsula due to human-induced activities. The tree has potential medicinal and economic benefits as a source of fuel and timber. It can fix nitrogen, a significant property that assists in desert rehabilitation. However, the lack of genomic information of Acacia pachyceras hampers its genetic study and breeding process. We performed paired-end sequencing of A. pachyceras at a depth of 120X to obtain raw sequences of 108.9 GB with a per base quality >Q30. Filtered raw data was assembled into a fasta file of 4 GB. The assembled genomic sequences consisted of 901,755 single sequence repeats (SSRs). In total 11,596 primer pairs were designed against these SSR motifs. The data generated provides baseline genomic information about the species and formulates a base for further sequencing of A. pachyceras through PACBio and HiC technologies. The novel developed SSR markers will facilitate genetic diversity and conservation studies for Acacia species.
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spelling pubmed-89338272022-03-20 Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz Habibi, Nazima Al Salameen, Fadila Rahman, Muhammed Kumar, Vinod Al Amad, Sami Shajan, Anisha Zakir, Farhana Abdul Razzack, Nasreem Tinwala, Waiel Hussain Data Brief Data Article Acacia tree population is declining in several countries of the world especially in the Arabian peninsula due to human-induced activities. The tree has potential medicinal and economic benefits as a source of fuel and timber. It can fix nitrogen, a significant property that assists in desert rehabilitation. However, the lack of genomic information of Acacia pachyceras hampers its genetic study and breeding process. We performed paired-end sequencing of A. pachyceras at a depth of 120X to obtain raw sequences of 108.9 GB with a per base quality >Q30. Filtered raw data was assembled into a fasta file of 4 GB. The assembled genomic sequences consisted of 901,755 single sequence repeats (SSRs). In total 11,596 primer pairs were designed against these SSR motifs. The data generated provides baseline genomic information about the species and formulates a base for further sequencing of A. pachyceras through PACBio and HiC technologies. The novel developed SSR markers will facilitate genetic diversity and conservation studies for Acacia species. Elsevier 2022-03-08 /pmc/articles/PMC8933827/ /pubmed/35313494 http://dx.doi.org/10.1016/j.dib.2022.108031 Text en © 2022 The Author(s). Published by Elsevier Inc. https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Data Article
Habibi, Nazima
Al Salameen, Fadila
Rahman, Muhammed
Kumar, Vinod
Al Amad, Sami
Shajan, Anisha
Zakir, Farhana
Abdul Razzack, Nasreem
Tinwala, Waiel Hussain
Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz
title Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz
title_full Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz
title_fullStr Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz
title_full_unstemmed Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz
title_short Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz
title_sort draft genome sequence and ssr mining data of acacia pachyceras schwartz
topic Data Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8933827/
https://www.ncbi.nlm.nih.gov/pubmed/35313494
http://dx.doi.org/10.1016/j.dib.2022.108031
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