Intraspecific variation within Castor bean (Ricinus communis L.) based on chloroplast genomes
Intraspecific variation within Castor bean (Ricinus communis L.) based on chloroplast genomes
The high usage of castor oil in industrial applications and bio-diesel production has led to an increase in castor bean (Ricinus communis L.) cultivation in many countries. Wild species present a source of genetic variation for germplasm improvement, often important because of their adaptation to a wide range of habitats and stresses. Chloroplast genomes are widely used in population genetics and evolutionary studies. Herein, we carried out plastome genome sequencing of 20 wild and cultivated castor bean accessions to examine plastome structural variations (PSVs). Further, single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels), were identified and plastome sequences used to infer phylogenetic relationships. All the chloroplast genomes were quadripartite, with a length between 162,673 bp and 163,210 bp, with 112 genes (78 protein coding genes; PCGs, 30 tRNAs, and four rRNAs). The chloroplast genomes where conserved in terms of structure and content, with no significant PSVs detected except for a slight inverted repeat (IR) contraction in one accession. A total of 162 SNPs and 92 InDels were uncovered across the plastomes, with an average SNP and InDel density of 0.99 and 0.56 per kb respectively. Some of the non-synonymous mutations caused amino acid changes in functional domains. Intergenic spacers trnE-UUC-trnT-GGU and AccD-psaI were identified as potential barcoding regions. The phylogenetic analyses and neighbor-joining network supported three distinct lineages in castor bean. Genetic diversity was greater in one clade than the other, with implications for identifying adaptive germplasm in the wild. These results demonstrate the genetic variations and phylogenetic relationships between the wild and cultivated lineages and add insights into the origin of cultivation and spread of castor bean.
Chloroplast genome, Conserved domain, InDels, Phylogenetic relationship, Plastome structural variations, SNPs/, Wild/cultivated germplasm
112779
Muraguri, Sammy
2708fa18-d994-4527-af33-376a5d6920f9
Xu, Wei
d012c621-8510-4ac3-bd83-9da7515b98d2
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Muchugi, Alice
359ffb85-9394-4d59-ad2c-08e9dc6ca4e2
Oluwaniyi, Adejobi
789452d9-d2cb-4bb0-b382-f1ad03131af5
Oyebanji, Oyetola
f5230eae-7933-4838-bb5f-eb2a0faeac17
Liu, Aizhong
608cf2dc-7202-47b2-a27d-c3a1303fce46
1 November 2020
Muraguri, Sammy
2708fa18-d994-4527-af33-376a5d6920f9
Xu, Wei
d012c621-8510-4ac3-bd83-9da7515b98d2
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Muchugi, Alice
359ffb85-9394-4d59-ad2c-08e9dc6ca4e2
Oluwaniyi, Adejobi
789452d9-d2cb-4bb0-b382-f1ad03131af5
Oyebanji, Oyetola
f5230eae-7933-4838-bb5f-eb2a0faeac17
Liu, Aizhong
608cf2dc-7202-47b2-a27d-c3a1303fce46
Muraguri, Sammy, Xu, Wei, Chapman, Mark, Muchugi, Alice, Oluwaniyi, Adejobi, Oyebanji, Oyetola and Liu, Aizhong
(2020)
Intraspecific variation within Castor bean (Ricinus communis L.) based on chloroplast genomes.
Industrial Crops and Products, 155, , [112779].
(doi:10.1016/j.indcrop.2020.112779).
Abstract
The high usage of castor oil in industrial applications and bio-diesel production has led to an increase in castor bean (Ricinus communis L.) cultivation in many countries. Wild species present a source of genetic variation for germplasm improvement, often important because of their adaptation to a wide range of habitats and stresses. Chloroplast genomes are widely used in population genetics and evolutionary studies. Herein, we carried out plastome genome sequencing of 20 wild and cultivated castor bean accessions to examine plastome structural variations (PSVs). Further, single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels), were identified and plastome sequences used to infer phylogenetic relationships. All the chloroplast genomes were quadripartite, with a length between 162,673 bp and 163,210 bp, with 112 genes (78 protein coding genes; PCGs, 30 tRNAs, and four rRNAs). The chloroplast genomes where conserved in terms of structure and content, with no significant PSVs detected except for a slight inverted repeat (IR) contraction in one accession. A total of 162 SNPs and 92 InDels were uncovered across the plastomes, with an average SNP and InDel density of 0.99 and 0.56 per kb respectively. Some of the non-synonymous mutations caused amino acid changes in functional domains. Intergenic spacers trnE-UUC-trnT-GGU and AccD-psaI were identified as potential barcoding regions. The phylogenetic analyses and neighbor-joining network supported three distinct lineages in castor bean. Genetic diversity was greater in one clade than the other, with implications for identifying adaptive germplasm in the wild. These results demonstrate the genetic variations and phylogenetic relationships between the wild and cultivated lineages and add insights into the origin of cultivation and spread of castor bean.
Text
MuraguriFinal
- Accepted Manuscript
More information
Accepted/In Press date: 9 July 2020
e-pub ahead of print date: 14 July 2020
Published date: 1 November 2020
Keywords:
Chloroplast genome, Conserved domain, InDels, Phylogenetic relationship, Plastome structural variations, SNPs/, Wild/cultivated germplasm
Identifiers
Local EPrints ID: 443219
URI: http://eprints.soton.ac.uk/id/eprint/443219
ISSN: 0926-6690
PURE UUID: e20fc276-8c17-4b16-99ec-1918c49b6bc8
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Date deposited: 17 Aug 2020 16:31
Last modified: 10 Jan 2022 06:07
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Contributors
Author:
Sammy Muraguri
Author:
Wei Xu
Author:
Alice Muchugi
Author:
Adejobi Oluwaniyi
Author:
Oyetola Oyebanji
Author:
Aizhong Liu
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