Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Abstract Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have...

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Autores principales:	Sajjad Asaf, Abdul Latif Khan, Muhammad Numan, Ahmed Al-Harrasi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/15db395cdc3049069c52fa7590226544
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spelling	oai:doaj.org-article:15db395cdc3049069c52fa75902265442021-12-02T14:26:54ZMangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae10.1038/s41598-021-83060-z2045-2322https://doaj.org/article/15db395cdc3049069c52fa75902265442021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83060-zhttps://doaj.org/toc/2045-2322Abstract Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.Sajjad AsafAbdul Latif KhanMuhammad NumanAhmed Al-HarrasiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sajjad Asaf Abdul Latif Khan Muhammad Numan Ahmed Al-Harrasi Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae
description	Abstract Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.
format	article
author	Sajjad Asaf Abdul Latif Khan Muhammad Numan Ahmed Al-Harrasi
author_facet	Sajjad Asaf Abdul Latif Khan Muhammad Numan Ahmed Al-Harrasi
author_sort	Sajjad Asaf
title	Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae
title_short	Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae
title_full	Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae
title_fullStr	Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae
title_full_unstemmed	Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae
title_sort	mangrove tree (avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family acanthaceae
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/15db395cdc3049069c52fa7590226544
work_keys_str_mv	AT sajjadasaf mangrovetreeavicenniamarinainsightintochloroplastgenomeevolutionarydivergenceanditscomparisonwithrelatedspeciesfromfamilyacanthaceae AT abdullatifkhan mangrovetreeavicenniamarinainsightintochloroplastgenomeevolutionarydivergenceanditscomparisonwithrelatedspeciesfromfamilyacanthaceae AT muhammadnuman mangrovetreeavicenniamarinainsightintochloroplastgenomeevolutionarydivergenceanditscomparisonwithrelatedspeciesfromfamilyacanthaceae AT ahmedalharrasi mangrovetreeavicenniamarinainsightintochloroplastgenomeevolutionarydivergenceanditscomparisonwithrelatedspeciesfromfamilyacanthaceae
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Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

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