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The complete chloroplast genome of Heteromorpha arborescens (Apiaceae).

ABSTRACT: Heteromorpha arborescens has long been recognized and cultivated as an important medicinal plant. We reported its complete plastid genome for the first time and reconstructed its phylogenetic position. The complete plastid genome was 157,172 bp in length with a typical quadripartite organization: a large single-copy (LSC) region of 86,436 bp, a small single-copy (SSC) region of 18,222 bp, and two inverted repeat regions (IRa and IRb), each of 26,257 bp. A total of 130 functional genes were recovered, consisting of 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis suggested that H. arborescens is sister to other species except Cetella arborescens in Apiaceae with strong ultrafast support.

SUBMITTER: Li H

PROVIDER: S-EPMC7781938 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Torilis scabra (Apiaceae).

Project description:Torilis scabra (Thunb.) DC. is widely distributed in China and Japan and has been introduced to North America. In this study, the complete chloroplast genome sequence of the T. scabra was obtained by de novo assembly using the NGS data. The chloroplast genome of T. scabra was 157,855 bp in length and divided into four distinct regions, such as large single-copy region (85,362 bp), small single-copy region (17,993 bp), and a pair of inverted repeat regions (27,250 bp). The genome annotation predicted a total of 127 genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with reported chloroplast genomes showed that T. scabra has a close genetic relationship with Anthriscus cerefolium.

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The complete chloroplast genome of Meeboldia yunnanensis (Apiaceae).

Project description:Meeboldia yunnanensis Wolff (Apiaceae) is a perennial species naturally distributed in Yunnan and Xizang. The complete chloroplast genome sequence of M. yunnanensis was generated by de novo assembly using whole-genome next-generation sequencing data. The complete chloroplast genome of M. yunnanensis was 154,865 bp in total sequence length and divided into four distinct regions: small single-copy region (17,370 bp), large single-copy region (84,641 bp), and a pair of inverted repeat regions (26,427 bp). The genome annotation displayed a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that M. yunnanensis has close relationship to Pterygopleurum neurophyllum.

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The complete chloroplast genome sequence of Ostericum koreanum (Apiaceae).

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| S-EPMC7800663 | biostudies-literature

The complete chloroplast genome sequence of Libanotis buchtormensis (Apiaceae).

Project description:Libanotis buchtormensis (Fisch.) DC. is one of the traditional Chinese herbal medicines in the Qinling District, while the genetic information is limited. In the study, we reported the complete chloroplast genome of L. buchtormensis using BGISEQ-500 sequencing data. The complete chloroplast genome was 147,036 bp in length with a GC content of 37.6%, consisting of four parts, namely LSC (91,969 bp), SSC (17,469 bp), and two IRs (18,799 bp in each). The cp genome contained 127 genes, including 83 CDS genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that L. buchtormensis was sister to Ledebouriella seseloides.

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The complete chloroplast genome sequence of Bupleurum chinense DC. (Apiaceae).

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The complete chloroplast genome sequence of Heracleum millefolium Diels (Apiaceae).

Project description:We assembled the complete chloroplast genome of Heracleum millefolium which is a traditional widely used medicinal plant in China. The whole genome is 150,025 bp in length which was divided into four subregions: a large single-copy region (93,645 bp), a pair of 19,458 bp inverted repeats regions, and a small single-copy region (17,464 bp), respectively. Additionally, the chloroplast genome of H. millefolium detected 128 genes, including 85 protein coding genes, 36 transfer RNAs, and eight ribosomal RNAs. The overall GC content of this chloroplast genome is 37.5% and the mean coverage value is 1752.4x. Phylogenetic analysis based on 17 chloroplast genomes dataset was conducted to clarify the relationships of the major clades in Apiaceae. The results strongly supported the monophyly of Heracleum and the closer relationship of H. millefolium and H. candicans.

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The complete chloroplast genome sequence of the medicinal plant, Angelica gigas (Apiaceae).

Project description:The complete chloroplast genome sequence of Angelica gigas, a traditional herbal plant used in treating diseases, was obtained by de novo assembly using illumina sequencing data (Illumina Inc., San Diego, CA). The circular molecule of the genome was constructed of four parts, with a size of 146,916?bp in total - a large single copy (LSC) region of 93,118?bp, a small single copy (SSC) region of 17,582?bp and two inverted repeat (IRa and IRb) regions of 18,108?bp each. There were a total of 113 annotated genes, including 80 protein-coding genes, 29 tRNA genes and four rRNA genes. The phylogenetic result acquired through maximum parsimony analysis showed that A. gigas is closely related with A. decursiva and Seseli montanum.

| S-EPMC7870150 | biostudies-literature

Chloroplast genome analyses of Caragana arborescens and Caragana opulens.

Project description:BackgroundNumerous species within the genus Caragana have high ecological and medicinal value. However, species identification based on morphological characteristics is quite complicated in the genus. To address this issue, we analyzed complete plastid genome data for the genus.ResultsWe obtained chloroplast genomes of two species, Caragana arborescens and Caragana opulens, using Illumina sequencing technology, with lengths of 129,473 bp and 132,815 bp, respectively. The absence of inverted repeat sequences in the two species indicated that they could be assigned to the inverted repeat-lacking clade (IRLC). The genomes included 111 distinct genes (4 rRNA genes, 31 tRNA genes, and 76 protein-coding genes). In addition, 16 genes containing introns were identified in the two genomes, the majority of which contained a single intron. Repeat analyses revealed 129 and 229 repeats in C. arborescens and C. opulens, respectively. C. arborescens and C. opulens genomes contained 277 and 265 simple sequence repeats, respectively. The two Caragana species exhibited similar codon usage patterns. rpl20-clpP, rps19-rpl2, and rpl23-ycf2 showed the highest nucleotide diversity (pi). In an analysis of sequence divergence, certain intergenic regions (matK-rbcL, psbM-petN, atpA-psbI, petA-psbL, psbE-petL, and rps7-rps12) were highly variable. A phylogenetic analysis showed that C. arborescens and C. opulens were related and clustered together with four other Caragana species. The genera Astragalus and Caragana were relatively closely related.ConclusionsThe present study provides valuable information about the chloroplast genomes of C. arborescens and C. opulens and lays a foundation for future phylogenetic research and molecular marker development.

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The complete chloroplast genome of Melanosciadium pimpinelloideum (Apiaceae), an endemic species of China.

Project description:Melanosciadium pimpinelloideum de Boiss. is an endemic species of China. Here, the complete chloroplast genome of M. pimpinelloideum is determined. The whole genome size is 164,431 bp in length, composed of a pair of inverted repeats (IRs) of 35,211 bp, a large single-copy region (LSC) of 76,444 bp and a small single-copy region (SSC) of 17,565 bp. The genome contains 136 genes, including 91 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis with the reported chloroplast genomes showed that M. pimpinelloideum and P. rhomboidea var. tenuiloba formed a well-supported clade, which nested in Angelica species. Logically, the result corroborated the previous treatment of P. rhomboidea var. tenuiloba.

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The complete chloroplast genome sequence of Sinolimprichtia alpina var. dissecta (Apiaceae).

Project description:Sinolimprichtia alpina var. dissecta is a plant variety which is characterized from S. alpina var. alpina in possessing characteristic, highly dissected bracteoles. In the current study, we have sequenced the complete chloroplast genome of S. alpina var. dissecta using the Illumina sequencing platform. The chloroplast genome is 156,719 bp in length, consisting of a LSC region of 95,625 bp, a SSC region of 10,500 bp, and a pair of inverted repeats (IR) regions of 25,297 bp. The GC content was 37.7%. A total of 126 unique genes were identified, including 81 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on 28 chloroplast genomes indicates that S. alpina var. dissecta is most closely related to Pterygopleurum neurophyllum.

| S-EPMC8018366 | biostudies-literature

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