AUTHOR=Wanga Vincent Okelo , Dong Xiang , Oulo Millicent Akinyi , Mkala Elijah Mbandi , Yang Jia-Xin , Onjalalaina Guy Eric , Gichua Moses Kirega , Kirika Paul Muigai , Gituru Robert Wahiti , Hu Guang-Wan , Wang Qing-Feng 

TITLE=Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement

JOURNAL=Frontiers in Plant Science

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.691833

DOI=10.3389/fpls.2021.691833

ISSN=1664-462X

ABSTRACT=<p><italic>Acanthochlamys</italic> P.C. Kao is a Chinese endemic monotypic genus, whereas <italic>Xerophyta</italic><bold>Juss</bold>. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of <italic>Acanthochlamys bracteata</italic> was sequenced and its genome structure compared with two African <italic>Xerophyta</italic> species (<italic>Xerophyta spekei</italic> and <italic>Xerophyta viscosa</italic>) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in <italic>A. bracteata</italic>, <italic>X. spekei</italic> and <italic>X. viscosa</italic> cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the <italic>A. bracteata</italic>, <italic>X. spekei</italic>, and <italic>X. viscosa</italic> cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that <italic>A. bracteata</italic> species has a closer genetic relationship to the genus <italic>Xerophyta</italic>. The present study reveals the complete chloroplast genome of <italic>A. bracteata</italic> and gives a genomic comparative analysis with the African species of <italic>Xerophyta</italic>. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.</p>