AUTHOR=Rono Peninah Cheptoo , Dong Xiang , Yang Jia-Xin , Mutie Fredrick Munyao , Oulo Millicent A. , Malombe Itambo , Kirika Paul M. , Hu Guang-Wan , Wang Qing-Feng 

TITLE=Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.560368

DOI=10.3389/fgene.2020.560368

ISSN=1664-8021

ABSTRACT=<p>The genus <italic>Alchemilla</italic> L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within <italic>Alchemilla</italic> is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of <italic>Alchemilla</italic>. The cp genomes of two African (<italic>Afromilla</italic>) species <italic>Alchemilla pedata</italic> and <italic>Alchemilla argyrophylla</italic> were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in <italic>A. pedata</italic> and <italic>A. argyrophylla</italic>, respectively. <italic>Alchemilla</italic> cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in <italic>A. pedata</italic> and <italic>A. argyrophylla</italic>, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in <italic>A. pedata</italic> and <italic>A. argyrophylla</italic>, respectively. Significantly, the loss of group II intron in <italic>atpF</italic> gene in <italic>Alchemilla</italic> species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of <italic>Alchemilla</italic> nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks &lt; 1) was detected with an average Ka/Ks value of 0.1322 in <italic>A. argyrophylla</italic> and 0.1418 in <italic>A. pedata</italic>. The availability of complete cp genome in the genus <italic>Alchemilla</italic> will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.</p>