Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance

The sago palm (Metroxylon sagu Rottb.) is an underappreciated essential food crop of the century and is deemed to be the ultimate solution to future food security issues globally. To grasp a better comprehension on the molecular basis of sago palm chloroplast, a complete characterization of the 157,...

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Main Authors: Chung, Hung Hui, Lim, Leonard Whye Kit, Hasnain, Bin Hussain
Format: E-Article
Language:English
Published: Elsevier 2020
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Online Access:http://ir.unimas.my/id/eprint/29631/1/Complete%20Chloroplast%20Genome%20Sequencing%20of%20Sago%20Palm%20%28Metroxylon%20sagu%20Rottb.%29%20-%20Copy.pdf
http://ir.unimas.my/id/eprint/29631/
https://www.journals.elsevier.com/gene-reports
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spelling my.unimas.ir.296312020-05-10T22:52:59Z http://ir.unimas.my/id/eprint/29631/ Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance Chung, Hung Hui Lim, Leonard Whye Kit Hasnain, Bin Hussain Q Science (General) QH Natural history The sago palm (Metroxylon sagu Rottb.) is an underappreciated essential food crop of the century and is deemed to be the ultimate solution to future food security issues globally. To grasp a better comprehension on the molecular basis of sago palm chloroplast, a complete characterization of the 157,300 bp chloroplast genome sequences (encompassing 85,257 bp large single copy region (LSC) and 17,533 bp small single copy region (SSC), sandwiched by a pair of 27,245 bp inverted repeats (IRs)) was performed. The genome houses 113 unique genes: 80 protein-coding genes, 29 tRNA genes and four ribosomal genes. The gene order, AT content and orientation of the M. sagu chloroplast genome closely resembles that of its congeneric species, M. warburgii. The distribution patterns of short and long repeats were also determined along with four highly variable regions, 216 mutation events (164 single nucleotide polymorphisms (SNPs) and 52 insertion/deletions (indels)) between the two Metroxylon genus members. The maximum likelihood phylogenetic tree had unravelled the close relationship of M. sagu, with its closest neighbour M. warburgii, together with other Calameae members like Pigafetta elata, Calamus caryotoides, and Salacca ramosiana. This study had dissected on the entire chloroplast genome of M. sagu and characterized the contents at the molecular level. It is anticipated that the yielded treasurable information will be channelled for species identification and evolutionary analysis within the Metroxylon genus in future. Elsevier 2020-03-25 E-Article PeerReviewed text en http://ir.unimas.my/id/eprint/29631/1/Complete%20Chloroplast%20Genome%20Sequencing%20of%20Sago%20Palm%20%28Metroxylon%20sagu%20Rottb.%29%20-%20Copy.pdf Chung, Hung Hui and Lim, Leonard Whye Kit and Hasnain, Bin Hussain (2020) Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance. Gene Reports, 2020. pp. 1-48. ISSN 2452-0144 https://www.journals.elsevier.com/gene-reports DOI:org/10.1016/j.genrep.2020.100662
institution Universiti Malaysia Sarawak
building Centre for Academic Information Services (CAIS)
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Sarawak
content_source UNIMAS Institutional Repository
url_provider http://ir.unimas.my/
language English
topic Q Science (General)
QH Natural history
spellingShingle Q Science (General)
QH Natural history
Chung, Hung Hui
Lim, Leonard Whye Kit
Hasnain, Bin Hussain
Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance
description The sago palm (Metroxylon sagu Rottb.) is an underappreciated essential food crop of the century and is deemed to be the ultimate solution to future food security issues globally. To grasp a better comprehension on the molecular basis of sago palm chloroplast, a complete characterization of the 157,300 bp chloroplast genome sequences (encompassing 85,257 bp large single copy region (LSC) and 17,533 bp small single copy region (SSC), sandwiched by a pair of 27,245 bp inverted repeats (IRs)) was performed. The genome houses 113 unique genes: 80 protein-coding genes, 29 tRNA genes and four ribosomal genes. The gene order, AT content and orientation of the M. sagu chloroplast genome closely resembles that of its congeneric species, M. warburgii. The distribution patterns of short and long repeats were also determined along with four highly variable regions, 216 mutation events (164 single nucleotide polymorphisms (SNPs) and 52 insertion/deletions (indels)) between the two Metroxylon genus members. The maximum likelihood phylogenetic tree had unravelled the close relationship of M. sagu, with its closest neighbour M. warburgii, together with other Calameae members like Pigafetta elata, Calamus caryotoides, and Salacca ramosiana. This study had dissected on the entire chloroplast genome of M. sagu and characterized the contents at the molecular level. It is anticipated that the yielded treasurable information will be channelled for species identification and evolutionary analysis within the Metroxylon genus in future.
format E-Article
author Chung, Hung Hui
Lim, Leonard Whye Kit
Hasnain, Bin Hussain
author_facet Chung, Hung Hui
Lim, Leonard Whye Kit
Hasnain, Bin Hussain
author_sort Chung, Hung Hui
title Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance
title_short Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance
title_full Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance
title_fullStr Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance
title_full_unstemmed Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance
title_sort complete chloroplast genome sequencing of sago palm (metroxylon sagu rottb.): molecular structures, comparative analysis and evolutionary significance
publisher Elsevier
publishDate 2020
url http://ir.unimas.my/id/eprint/29631/1/Complete%20Chloroplast%20Genome%20Sequencing%20of%20Sago%20Palm%20%28Metroxylon%20sagu%20Rottb.%29%20-%20Copy.pdf
http://ir.unimas.my/id/eprint/29631/
https://www.journals.elsevier.com/gene-reports
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