Dataset Information

The complete chloroplast genome sequence of Ficus hirta (Moraceae).

ABSTRACT: The dry root (Radix Fici Hirtae) of Ficus hirta has been used as a traditional herbal medicine in Ling nan regions of China for a long time. As its large market demand, the wild resources of F. hirta have sharply reduced. It is necessary to conduct the study of conservation genetics. However, there is still lack of complete genome information for the research on evolutionary biology, population genetics and phylogeography of this species. Here, we sequenced the complete chloroplast (CP) genome of F. hirta using Next Generation Sequencing technology (NGS). The CP genome of F. hirta is 160,374?bp in length, which contains a large single-copy (LSC) region of 88,446?bp, a small sing-copy (SSC) region of 18,134?bp, and two inverted repeat (IRa and IRb) regions of 26,897?bp. A total of 130 genes were successfully annotated containing 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis support genus Ficus is monophyletic and F. hirta is closely related to F. carica within this genus.

SUBMITTER: Liu Y

PROVIDER: S-EPMC7707796 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of Ficus hirta (Moraceae).

Liu Yinrong Y Chen Wenna W Li Fang F Li Chan C Xie Xuena X Chao Zhi Z Tian Enwei E

Mitochondrial DNA. Part B, Resources 20191113 2

The dry root (Radix Fici Hirtae) of Ficus hirta has been used as a traditional herbal medicine in Ling nan regions of China for a long time. As its large market demand, the wild resources of F. hirta have sharply reduced. It is necessary to conduct the study of conservation genetics. However, there is still lack of complete genome information for the research on evolutionary biology, population genetics and phylogeography of this species. Here, we sequenced the complete chloroplast ...[more]

PMID: 33366308

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Project description:Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F. sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 (F. dinganensis and F. howii) to 190 (F. polynervis), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes (accD, clpP, ndhK, rbcL, rpl20, rpl22, rpl23, rpoC1, rps15, and rps4) which exhibited potential positive selective signatures. Five hypervariable genic regions (rps15, ycf1, rpoA, ndhF, and rpl22) and five hypervariable intergenic regions (trnH-GUG-psbA, rpl32-trnL-UAG, psbZ-trnG-GCC, trnK-UUU-rps16 and ndhF-rpl32) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus, despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F. sarmentosa complex and F. auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.

Dataset Information

The complete chloroplast genome sequence of Ficus hirta (Moraceae).

Publications

The complete chloroplast genome sequence of <i>Ficus hirta</i> (Moraceae).

Similar Datasets

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