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Genome survey and genetic characterization of Acacia pachyceras O. Schwartz

Acacia pachyceras O. Schwartz (Leguminoseae), a woody tree growing in Kuwait is critically endangered. High throughput genomic research is immediately needed to formulate effective conservation strategies for its rehabilitation. We therefore, performed a genome survey analysis of the species. Whole...

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Autores principales: Habibi, Nazima, Al Salameen, Fadila, Vyas, Nishant, Rahman, Muhammad, Kumar, Vinod, Shajan, Anisha, Zakir, Farhana, Razzack, Nasreem Abdul, Al Doaij, Bashayer
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9979705/
https://www.ncbi.nlm.nih.gov/pubmed/36875582
http://dx.doi.org/10.3389/fpls.2023.1062401
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author Habibi, Nazima
Al Salameen, Fadila
Vyas, Nishant
Rahman, Muhammad
Kumar, Vinod
Shajan, Anisha
Zakir, Farhana
Razzack, Nasreem Abdul
Al Doaij, Bashayer
author_facet Habibi, Nazima
Al Salameen, Fadila
Vyas, Nishant
Rahman, Muhammad
Kumar, Vinod
Shajan, Anisha
Zakir, Farhana
Razzack, Nasreem Abdul
Al Doaij, Bashayer
author_sort Habibi, Nazima
collection PubMed
description Acacia pachyceras O. Schwartz (Leguminoseae), a woody tree growing in Kuwait is critically endangered. High throughput genomic research is immediately needed to formulate effective conservation strategies for its rehabilitation. We therefore, performed a genome survey analysis of the species. Whole genome sequencing generated ~97 Gb of raw reads (92x coverage) with a per base quality score above Q30. The k-mer analysis (17 mer) revealed its genome to be 720Mb in size with an average guanine-cytosine (GC) ratio of 35%. The assembled genome was analyzed for repeat regions (45.4%-interspersed repeats; 9%-retroelements; 2%-DNA transposons). BUSCO assessment of completeness of genome identified 93% of assembly to be complete. Gene alignments in BRAKER2 yielded 34,374 transcripts corresponding to 33,650 genes. Average length of coding sequences and protein sequences were recorded as 1,027nts and 342aa, respectively. GMATA software filtered a total of 901,755 simple sequence repeats (SSRs) regions against which 11,181 unique primers were designed. A subset of 110 SSR primers were PCR validated and demonstrated for its application in genetic diversity analysis of Acacia. The SSR primers successfully amplified A. gerrardii seedlings DNA depicting cross transferability among species. The principal coordinate analysis and the split decomposition tree (bootstrapping runs of 1000 replicates) distributed the Acacia genotypes into two clusters. The flow cytometry analysis revealed the A. pachyceras genome to be polyploid (6x). The DNA content was predicted as 2.46 pg, 1.23 pg, and 0.41 pg corresponding to 2C DNA, 1C DNA and 1Cx DNA, respectively. The results provide a base for further high throughput genomic studies and molecular breeding for its conservation.
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spelling pubmed-99797052023-03-03 Genome survey and genetic characterization of Acacia pachyceras O. Schwartz Habibi, Nazima Al Salameen, Fadila Vyas, Nishant Rahman, Muhammad Kumar, Vinod Shajan, Anisha Zakir, Farhana Razzack, Nasreem Abdul Al Doaij, Bashayer Front Plant Sci Plant Science Acacia pachyceras O. Schwartz (Leguminoseae), a woody tree growing in Kuwait is critically endangered. High throughput genomic research is immediately needed to formulate effective conservation strategies for its rehabilitation. We therefore, performed a genome survey analysis of the species. Whole genome sequencing generated ~97 Gb of raw reads (92x coverage) with a per base quality score above Q30. The k-mer analysis (17 mer) revealed its genome to be 720Mb in size with an average guanine-cytosine (GC) ratio of 35%. The assembled genome was analyzed for repeat regions (45.4%-interspersed repeats; 9%-retroelements; 2%-DNA transposons). BUSCO assessment of completeness of genome identified 93% of assembly to be complete. Gene alignments in BRAKER2 yielded 34,374 transcripts corresponding to 33,650 genes. Average length of coding sequences and protein sequences were recorded as 1,027nts and 342aa, respectively. GMATA software filtered a total of 901,755 simple sequence repeats (SSRs) regions against which 11,181 unique primers were designed. A subset of 110 SSR primers were PCR validated and demonstrated for its application in genetic diversity analysis of Acacia. The SSR primers successfully amplified A. gerrardii seedlings DNA depicting cross transferability among species. The principal coordinate analysis and the split decomposition tree (bootstrapping runs of 1000 replicates) distributed the Acacia genotypes into two clusters. The flow cytometry analysis revealed the A. pachyceras genome to be polyploid (6x). The DNA content was predicted as 2.46 pg, 1.23 pg, and 0.41 pg corresponding to 2C DNA, 1C DNA and 1Cx DNA, respectively. The results provide a base for further high throughput genomic studies and molecular breeding for its conservation. Frontiers Media S.A. 2023-02-16 /pmc/articles/PMC9979705/ /pubmed/36875582 http://dx.doi.org/10.3389/fpls.2023.1062401 Text en Copyright © 2023 Habibi, Al Salameen, Vyas, Rahman, Kumar, Shajan, Zakir, Razzack and Al Doaij https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Habibi, Nazima
Al Salameen, Fadila
Vyas, Nishant
Rahman, Muhammad
Kumar, Vinod
Shajan, Anisha
Zakir, Farhana
Razzack, Nasreem Abdul
Al Doaij, Bashayer
Genome survey and genetic characterization of Acacia pachyceras O. Schwartz
title Genome survey and genetic characterization of Acacia pachyceras O. Schwartz
title_full Genome survey and genetic characterization of Acacia pachyceras O. Schwartz
title_fullStr Genome survey and genetic characterization of Acacia pachyceras O. Schwartz
title_full_unstemmed Genome survey and genetic characterization of Acacia pachyceras O. Schwartz
title_short Genome survey and genetic characterization of Acacia pachyceras O. Schwartz
title_sort genome survey and genetic characterization of acacia pachyceras o. schwartz
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9979705/
https://www.ncbi.nlm.nih.gov/pubmed/36875582
http://dx.doi.org/10.3389/fpls.2023.1062401
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