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Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae
Joint Authors
Yaradua, Samaila S.
Alzahrani, Dhafer A.
Albokhary, Enas J.
Abba, Abidina
Bello, Abubakar
Source
Issue
Vol. 2019, Issue 2019 (31 Dec. 2019), pp.1-17, 17 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2019-08-06
Country of Publication
Egypt
No. of Pages
17
Main Subjects
Abstract EN
The complete chloroplast genome of J.
flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae.
NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data.
The cp genome of J.
flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp).
There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions.
The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer.
The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region.
All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC.
Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection.
The phylogenetic analysis revealed that Justiceae is sister to Ruellieae.
This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J.
flava as well as resolving phylogenetic relationships within the core Acanthaceae.
American Psychological Association (APA)
Yaradua, Samaila S.& Alzahrani, Dhafer A.& Albokhary, Enas J.& Abba, Abidina& Bello, Abubakar. 2019. Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. BioMed Research International،Vol. 2019, no. 2019, pp.1-17.
https://search.emarefa.net/detail/BIM-1125304
Modern Language Association (MLA)
Yaradua, Samaila S.…[et al.]. Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. BioMed Research International No. 2019 (2019), pp.1-17.
https://search.emarefa.net/detail/BIM-1125304
American Medical Association (AMA)
Yaradua, Samaila S.& Alzahrani, Dhafer A.& Albokhary, Enas J.& Abba, Abidina& Bello, Abubakar. Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. BioMed Research International. 2019. Vol. 2019, no. 2019, pp.1-17.
https://search.emarefa.net/detail/BIM-1125304
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1125304