scholarly journals Chloroplast genome features and phylogenomic placement of Lespedeza bicolor (Fabaceae)

2020 ◽  
Vol 5 (2) ◽  
pp. 1870-1871
Author(s):  
Shou-Jin Fan ◽  
Yang Yu ◽  
Wen-Qing Li ◽  
Xiu-Xiu Guo ◽  
Xiao-Jian Qu
Keyword(s):  
Chloroplast Genome ◽  
Genome Features ◽  
Lespedeza Bicolor

scholarly journals Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

2021 ◽  
Vol 12 ◽  
Author(s):  
Abbas Jamal ◽  
Jun Wen ◽  
Zhi-Yao Ma ◽  
Ibrar Ahmed ◽  
Abdullah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Eastern China ◽  
Gc Content ◽  
Quaternary Period ◽  
Medicinal Uses ◽  
Endemic Genus ◽  
Chloroplast Genomes ◽  
Genome Features ◽  
Forest Regions ◽  
Genome Analyses

Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

scholarly journals Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

PLoS ONE ◽  
2020 ◽  
Vol 15 (9) ◽  
pp. e0239823
Author(s):  
Bin Zhu ◽  
Qun Feng ◽  
Jie Yu ◽  
Yu Yu ◽  
Xiaoxiang Zhu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Edible Plant ◽  
Houttuynia Cordata ◽  
Genome Features

scholarly journals Chloroplast genome features and phylogenomic placement of Sorbus hupehensis var. paucijuga (Rosaceae)

2021 ◽  
Vol 6 (3) ◽  
pp. 1068-1070
Author(s):  
Dan Liu ◽  
Xiao-Man Xie ◽  
Yi-Zeng Lu ◽  
Feng Li ◽  
Jian Zheng ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Features

scholarly journals Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 441
Author(s):  
Shixiong Ding ◽  
Xiang Dong ◽  
Jiaxin Yang ◽  
Chunce Guo ◽  
Binbin Cao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Adaptive Evolution ◽  
Single Copy ◽  
Evolutionary Conservation ◽  
Central China ◽  
Rrna Genes ◽  
Trna Genes ◽  
Complete Chloroplast Genome ◽  
Genome Features

Clethra fargesii, an essential ecological and endemic woody plant of the genus Clethra in Clethraceae, is widely distributed in Central China. So far, there have been a paucity of studies on its chloroplast genome. In the present study, we sequenced and assembled the complete chloroplast genome of C. fargesii. We also analyzed the chloroplast genome features and compared them to Clethra delavayi and other closely related species in Ericales. The complete chloroplast genome is 157,486 bp in length, including a large single-copy (LSC) region of 87,034 bp and a small single-copy (SSC) region of 18,492 bp, separated by a pair of inverted repeat (IR) regions of 25,980 bp. The GC content of the whole genome is 37.3%, while those in LSC, SSC, and IR regions are 35.4%, 30.7%, and 43.0%, respectively. The chloroplast genome of C. fargesii encodes 132 genes in total, including 87 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. A total of 26,407 codons and 73 SSRs were identified in C. fargesii chloroplast genome. Additionally, we postulated and demonstrated that the structure of the chloroplast genome in Clethra species may present evolutionary conservation based on the comparative analysis of genome features and genome alignment among eight Ericales species. The low Pi values revealed evolutionary conservation based on the nucleotide diversity analysis of chloroplast genome in two Clethra species. The low selection pressure was shown by a few positively selected genes by adaptive evolution analysis using 80 coding sequences (CDSs) of the chloroplast genomes of two Clethra species. The phylogenetic tree showed that Clethraceae and Ericaceae are sister clades, which reconfirm the previous hypothesis that Clethra is highly conserved in the chloroplast genome using 75 CDSs of chloroplast genome among 40 species. The genome information and analysis results presented in this study are valuable for further study on the intraspecies identification, biogeographic analysis, and phylogenetic relationship in Clethraceae.

scholarly journals Comparison of chloroplast genomes of Gynura species: sequence variation, genome rearrangement and divergence studies

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Tianyu Han ◽  
Mimi Li ◽  
Jiawei Li ◽  
Han Lv ◽  
Bingru Ren ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Genome Rearrangement ◽  
Divergence Time ◽  
Purifying Selection ◽  
Genome Sequences ◽  
Chloroplast Genomes ◽  
Genome Features ◽  
Relationship Of

Abstract Background Some Gynura species have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hybridizations. For flowerings plants, chloroplast genomes have been used to solve many phylogenetic relationships. To date, the chloroplast genome sequences of 4 genera of the tribe Senecioneae have been uploaded to GenBank. The internal relationships within the genus Gynura and the relationship of the genus Gynura with other genera in the tribe Senecioneae need further research. Results The chloroplast genomes of 4 Gynura species were sequenced, assembled and annotated. In comparison with those of 12 other Senecioneae species, the Gynura chloroplast genome features were analysed in detail. Subsequently, differences in the microsatellite and repeat types in the tribe were found. From the comparison, it was found that IR expansion and contraction are conserved in the genera Gynura, Dendrosenecio and Ligularia. Compared to other regions on the chloroplast genome, the region from 25,000 to 50,000 bp was not conserved. Seven ndh genes in this region are under purifying selection, with small changes in amino acids. The whole chloroplast genome sequences of 16 Senecioneae species were used to build a phylogenetic tree. Based on the oldest Artemisia pollen fossil, the divergence time was estimated. Conclusions Sequencing the chloroplast genomes of 4 Gynura species helps us to solve many problems. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were evaluated by comparing their chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia was different from that observed previous work. In a previous phylogenetic tree, the genus Ligularia belonged to the Tussilagininae subtribe, which was in a lineage that diverged earlier than other genera. Further morphology and genome-wide analyses are needed to clarify the genus relationships.

scholarly journals Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 476 ◽  
Author(s):  
Shabina Iram ◽  
Muhammad Qasim Hayat ◽  
Muhammad Tahir ◽  
Alvina Gul ◽  
Abdullah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Cost Effective ◽  
Single Copy ◽  
Protein Coding ◽  
Important Species ◽  
Mutational Hotspots ◽  
Genome Features ◽  
Artemisia Scoparia ◽  
Chloroplast Genome Sequence

Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.

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