Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships
The genus Alchemilla 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 Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient...
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Frontiers Media S.A.
2020-12-01
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Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.560368/full |
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doaj-356ea9171e51402e9668476e4e30d3d7 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Peninah Cheptoo Rono Peninah Cheptoo Rono Peninah Cheptoo Rono Xiang Dong Xiang Dong Xiang Dong Jia-Xin Yang Jia-Xin Yang Fredrick Munyao Mutie Fredrick Munyao Mutie Fredrick Munyao Mutie Millicent A. Oulo Millicent A. Oulo Millicent A. Oulo Itambo Malombe Paul M. Kirika Guang-Wan Hu Guang-Wan Hu Qing-Feng Wang Qing-Feng Wang |
spellingShingle |
Peninah Cheptoo Rono Peninah Cheptoo Rono Peninah Cheptoo Rono Xiang Dong Xiang Dong Xiang Dong Jia-Xin Yang Jia-Xin Yang Fredrick Munyao Mutie Fredrick Munyao Mutie Fredrick Munyao Mutie Millicent A. Oulo Millicent A. Oulo Millicent A. Oulo Itambo Malombe Paul M. Kirika Guang-Wan Hu Guang-Wan Hu Qing-Feng Wang Qing-Feng Wang Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships Frontiers in Genetics Alchemilla argyrophylla A. pedata chloroplast genome phylogenetic Rosaceae |
author_facet |
Peninah Cheptoo Rono Peninah Cheptoo Rono Peninah Cheptoo Rono Xiang Dong Xiang Dong Xiang Dong Jia-Xin Yang Jia-Xin Yang Fredrick Munyao Mutie Fredrick Munyao Mutie Fredrick Munyao Mutie Millicent A. Oulo Millicent A. Oulo Millicent A. Oulo Itambo Malombe Paul M. Kirika Guang-Wan Hu Guang-Wan Hu Qing-Feng Wang Qing-Feng Wang |
author_sort |
Peninah Cheptoo Rono |
title |
Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships |
title_short |
Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships |
title_full |
Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships |
title_fullStr |
Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships |
title_full_unstemmed |
Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships |
title_sort |
initial complete chloroplast genomes of alchemilla (rosaceae): comparative analysis and phylogenetic relationships |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2020-12-01 |
description |
The genus Alchemilla 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 Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla 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 A. pedata and A. argyrophylla, respectively. Alchemilla 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 A. pedata and A. argyrophylla, 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 A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla 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 Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae. |
topic |
Alchemilla argyrophylla A. pedata chloroplast genome phylogenetic Rosaceae |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2020.560368/full |
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doaj-356ea9171e51402e9668476e4e30d3d72020-12-09T06:22:45ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-12-011110.3389/fgene.2020.560368560368Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic RelationshipsPeninah Cheptoo Rono0Peninah Cheptoo Rono1Peninah Cheptoo Rono2Xiang Dong3Xiang Dong4Xiang Dong5Jia-Xin Yang6Jia-Xin Yang7Fredrick Munyao Mutie8Fredrick Munyao Mutie9Fredrick Munyao Mutie10Millicent A. Oulo11Millicent A. Oulo12Millicent A. Oulo13Itambo Malombe14Paul M. Kirika15Guang-Wan Hu16Guang-Wan Hu17Qing-Feng Wang18Qing-Feng Wang19CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaEast African Herbarium, National Museums of Kenya, Nairobi, KenyaEast African Herbarium, National Museums of Kenya, Nairobi, KenyaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaThe genus Alchemilla 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 Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla 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 A. pedata and A. argyrophylla, respectively. Alchemilla 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 A. pedata and A. argyrophylla, 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 A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla 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 Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.https://www.frontiersin.org/articles/10.3389/fgene.2020.560368/fullAlchemilla argyrophyllaA. pedatachloroplast genomephylogeneticRosaceae |