Comparative Chloroplast Genomics in Phyllanthaceae Species

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http://hdl.handle.net/10138/333835

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Rehman , U , Sultana , N , Abdullah , Jamal , A , Muzaffar , M & Poczai , P 2021 , ' Comparative Chloroplast Genomics in Phyllanthaceae Species ' , Diversity-Bazel , vol. 13 , no. 9 , 403 . https://doi.org/10.3390/d13090403

Title: Comparative Chloroplast Genomics in Phyllanthaceae Species
Author: Rehman, Umar; Sultana, Nighat; Abdullah,; Jamal, Abbas; Muzaffar, Maryam; Poczai, Péter
Contributor: University of Helsinki, Botany
Date: 2021
Language: eng
Number of pages: 18
Belongs to series: Diversity-Bazel
ISSN: 1424-2818
URI: http://hdl.handle.net/10138/333835
Abstract: Family Phyllanthaceae belongs to the eudicot order Malpighiales, and its species are herbs, shrubs, and trees that are mostly distributed in tropical regions. Here, we elucidate the molecular evolution of the chloroplast genome in Phyllanthaceae and identify the polymorphic loci for phylogenetic inference. We de novo assembled the chloroplast genomes of three Phyllanthaceae species, i.e., Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius, and compared them with six other previously reported genomes. All species comprised two inverted repeat regions (size range 23,921–27,128 bp) that separated large single-copy (83,627–89,932 bp) and small single-copy (17,424–19,441 bp) regions. Chloroplast genomes contained 111–112 unique genes, including 77–78 protein-coding, 30 tRNAs, and 4 rRNAs. The deletion/pseudogenization of rps16 genes was found in only two species. High variability was seen in the number of oligonucleotide repeats, while guanine-cytosine contents, codon usage, amino acid frequency, simple sequence repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions were similar. The transition substitutions were higher in coding sequences than in non-coding sequences. Phylogenetic analysis revealed the polyphyletic nature of the genus Phyllanthus. The polymorphic proteincoding genes, including rpl22, ycf1, matK, ndhF, and rps15, were also determined, which may be helpful for reconstructing the high-resolution phylogenetic tree of the family Phyllanthaceae. Overall, the study provides insight into the chloroplast genome evolution in Phyllanthaceae.
Subject: 11831 Plant biology
chloroplast genome
Phyllanthaceae
Leptopus
Phyllanthus
polymorphic loci
polyphyletic relationships
PHYLOGENETIC ANALYSIS
MATERNAL INHERITANCE
EMBLICA L.
SEQUENCE
DNA
ALIGNMENT
DYNAMICS
GENES
PHYLOGENOMICS
ORGANIZATION
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