Dataset Information

Complete chloroplast genome of Nyctocalos pinnatum: chloroplast features and phylogenetic relationships within Bignoniaceae.

ABSTRACT: Nyctocalos is a genus of flowering lianas belonging to the family Bignoniaceae, and occurring from South-Central China to Malesia. In this study, we assembled the first complete chloroplast genome of N. pinnatum. The total length of the chloroplast genome is 159591 bp, with a GC content of 38.04%, which includes a pair of inverted repeats of 30,480 bp, a small single-copy region of 12,774 bp and a large single-copy region of 85,857 bp. The chloroplast genome contains 135 genes, consisting of 89 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. We constructed a phylogenomic tree with representative chloroplast genomes from Bignoniaceae. N. pinnatum is revealed to be sister to Oroxylum in the tribe Oroxyleae, with a high bootstrap support. This is the first chloroplast genome assembled in Nyctocalos, and it provides essential information for further ecology and evolutionary studies in this genus and Bignoniaceae.

SUBMITTER: Fan H

PROVIDER: S-EPMC9225756 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Complete chloroplast genome of Nyctocalos pinnatum: chloroplast features and phylogenetic relationships within Bignoniaceae.

Fan Huan H Li Jinyue J Landrein Sven S

Mitochondrial DNA. Part B, Resources 20220614 6

Nyctocalos is a genus of flowering lianas belonging to the family Bignoniaceae, and occurring from South-Central China to Malesia. In this study, we assembled the first complete chloroplast genome of N. pinnatum. The total length of the chloroplast genome is 159591 bp, with a GC content of 38.04%, which includes a pair of inverted repeats of 30,480 bp, a small single-copy region of 12,774 bp and a large single-copy region of 85,857 bp. The chloroplast genome contains 135 genes, con ...[more]

PMID: 35756448

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Project description:Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite or whorled leaves. C. bungei, C. fargesii f. duclouxii and C. fargesii are sources of traditional precious wood in China, known as the "kings of wood". Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within Catalpa. Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus Catalpa and analyzed their basic structure and evolutionary relationships. The chloroplast genome of Catalpa shows a typical tetrad structure with a total length ranging from 157,765 bp (C. fargesii) to 158,355 bp (C. ovata). The length of the large single-copy (LSC) region ranges from 84,599 bp (C. fargesii) to 85,004 bp (C. ovata), that of the small single-copy (SSC) region ranges from 12,662 bp (C. fargesii) to 12,675 bp (C. ovata), and that of the inverted repeat (IR) regions ranges from 30,252 bp (C. fargesii) to 30,338 bp (C. ovata). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus Catalpa formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of Catalpa, which will facilitate future research efforts.

Project description:Vicatia thibetica de Boiss.: a herb in the family Apiaceae, has been used for over a hundred years as an essential medicinal and edible plant in the Bai ethnic group of Dali City. However, due to the lack of study on plastid genomes of V. thibetica, studies of comparison and phylogeny with other related species remain scarce. In the current study, we assembled, annotated, and characterized the entire chloroplast (cp) genome of V. thibetica through high-throughput sequencing for the first time, compared with published whole chloroplast genomes from the same family. A phylogenetic analysis of the chloroplast genome has also been performed. The whole chloroplast genome of V. thibetica was 145,796 in size and consisted of a large single-copy region (LSC; 92,186 bp), a small single-copy region (SSC; 17,452 bp), and a pair of inverted repeat regions (IRs; 18,079 bp) forming a circular quadripartite structure. Annotation resulted in 128 genes, including 84 protein-coding genes (PCGs), 35 transfer RNA genes (tRNAs), eight ribosomal genes (rRNAs), and one pseudogene. Repeat sequence analysis displayed V. thibetica plastid genome contains 75 simple repeats, 37 long repeats, and 29 tandem repeats. Compared with the cp genome of other Apiaceae species, a common feature was that the IR regions of the genome were more conservative compared to the LSC and SSC regions. Highly variable hotspots included rps16, ndhC-trnV-UAC, clpP, ycf1, and ndhB in the genomes, which supply valuable molecular markers for phylogeny, identification, and classification in the Apiaceae family. The results of phylogenetic analysis strongly supported the genus Vicatia as an independent genus in the family Apiaceae, in which the closest affinities to the related species of Angelica, Peucedanum, and Ligusticum were observed. In conclusion, the first chloroplast genome of Vicatia reported in this study may improve our understanding of phylogenetic relationship of different genera of Apiaceae. In addition, the current data will be valuable as chloroplast genomic resource for species identification and population genetics.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-022-01154-y.

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Project description:Zingiberaceae is taxonomically complex family where species are perennial herb. However, lack of chloroplast genomic information severely hinders our understanding of Zingiberaceae species in the research of evolution and phylogenetic relationships. In this study, the complete chloroplast (cp) genomes of fourteen Curcuma species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the 25 Zingiberaceae species. In each Zingiberaceae species, the 25 complete chloroplast genomes ranging from 155,890 bp (Zingiber spectabile) to 164,101 bp (Lanxangia tsaoko) contained 111 genes consisting of 77 protein coding genes, 4 ribosomal RNAs and 30 transfer RNAs. These chloroplast genomes are similar to most angiosperm that consisted of a four-part circular DNA molecules. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were found. Six divergent hotspots regions (matK-trnk, Rps16-trnQ, petN-psbM, rpl32, ndhA, and ycf1) were identified in the 25 Zingiberaceae chloroplast genomes, which could be potential molecular markers. In addition to Wurfbainia longiligularis, the ψycf1 was discovered among the 25 Zingiberaceae species. The shared protein coding genes from 52 Zingiberales plants and four other family species as out groups were used to construct phylogenetic trees distinguished by maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) and showed that Musaceae was the basal group in Zingiberales, and Curcuma had a close relationship with Stahlianthu. Besides this, Curcuma flaviflora was clustered together with Zingiber. Its distribution area (Southeast Asia) overlaps with the latter. Maybe hybridization occur in related groups within the same region. This may explain why Zingiberaceae species have a complex phylogeny, and more samples and genetic data were necessary to confirm their relationship. This study provide the reliable information and high-quality chloroplast genomes and genome resources for future Zingiberaceae research.

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Dataset Information

Complete chloroplast genome of Nyctocalos pinnatum: chloroplast features and phylogenetic relationships within Bignoniaceae.

Publications

Complete chloroplast genome of <i>Nyctocalos pinnatum</i>: chloroplast features and phylogenetic relationships within Bignoniaceae.

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