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Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus

The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities bet...

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Autores principales: Xia, Xi, Peng, Jingyu, Yang, Lin, Zhao, Xueli, Duan, Anan, Wang, Dawei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9224849/
https://www.ncbi.nlm.nih.gov/pubmed/35743879
http://dx.doi.org/10.3390/life12060848
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author Xia, Xi
Peng, Jingyu
Yang, Lin
Zhao, Xueli
Duan, Anan
Wang, Dawei
author_facet Xia, Xi
Peng, Jingyu
Yang, Lin
Zhao, Xueli
Duan, Anan
Wang, Dawei
author_sort Xia, Xi
collection PubMed
description The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89–104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.
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spelling pubmed-92248492022-06-24 Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus Xia, Xi Peng, Jingyu Yang, Lin Zhao, Xueli Duan, Anan Wang, Dawei Life (Basel) Article The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89–104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus. MDPI 2022-06-07 /pmc/articles/PMC9224849/ /pubmed/35743879 http://dx.doi.org/10.3390/life12060848 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Xia, Xi
Peng, Jingyu
Yang, Lin
Zhao, Xueli
Duan, Anan
Wang, Dawei
Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus
title Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus
title_full Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus
title_fullStr Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus
title_full_unstemmed Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus
title_short Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus
title_sort comparative analysis of the complete chloroplast genomes of eight ficus species and insights into the phylogenetic relationships of ficus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9224849/
https://www.ncbi.nlm.nih.gov/pubmed/35743879
http://dx.doi.org/10.3390/life12060848
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