The complete chloroplast genome of a Chinese endemic poorly known species Campylotropis grandifolia (Fabaceae).
Ontology highlight
ABSTRACT:
SUBMITTER: Duan H
PROVIDER: S-EPMC8751491 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Ormosia nuda is a legume species endemic to China. The chloroplast genome (plastome) of this species was assembled in this study. The total plastome size is 173,789 bp in length, containing a large single-copy (LSC) region of 73,847 bp, a small single-copy (SSC) region of 18,744 bp, and two inverted repeat (IR) regions of 40,599 bp which have expanded about 15 kb into LSC. The plastome encodes a total of 111 unique genes, including 77 protein-coding, 30 tRNA, and 4 rRNA genes. Phylogenetic analysis well resolved that O. nuda clustered with O. xylocarpa and O. emarginata. The plastome of O. nuda will provide informative genomic resources for further phylogenetic studies.
| S-EPMC8218860 | biostudies-literature
Project description:Corydalis trisecta Franch. is an endemic plant found in China. In this study, we presented the first complete chloroplast genome of C. trisecta, which was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome was 161,410?bp in length, with a GC content of 41.4% in total. Its structure contained a large single copy (LSC) region of 89,127?bp and a small single copy (SSC) region of 16,993?bp, which were separated by a pair of extremely inverted repeats (IRs) of 27,645?bp each, with GC content 39.8, 87.2, and 45.2%, respectively. The phylogenetic analysis indicated that C. triscta was sister to Lamprocapons spectabilis in Papaveraceae.
| S-EPMC7687375 | biostudies-literature
Project description:Ziziphus Mill. (Rhamnaceae) is comprised of about 170 species that are mainly distributed in tropical to subtropical regions, with few in the temperate zone. Several Ziziphus fruit tree species are important energy, nutrient, and medicinal resources for human populations, particularly for those living in rural regions. To date, limited genomic information is available for this genus. Here, we assembled the complete chloroplast genomes of four best known Ziziphus species, i.e., Ziziphus jujuba, Ziziphus acidojujuba, Ziziphus mauritiana, and Ziziphus spina-christi, based on the Illumina Paired-end sequencing method. The chloroplast genomes of the four Ziziphus species are all very similar to one another, and exhibit structural, gene content, and order characteristics that are similar to other flowering plants. The entire chloroplast genome encodes 113 predicted unique genes (85 protein-coding genes, 8 rRNA, and 37 tRNA), 17 of which are duplicated in the inverted repeat regions. Rich single sequence repeats loci (217) were detected in Z. jujuba and 106 SSR loci, composed of A/T, displayed polymorphism across the four species by comparative genomic analysis. We found only four genes under positive selection between Z. jujuba and Z. acidojujuba, and two genes for Z. mauritiana vs. Z. spina-christi, respectively, while half of the 78 protein-coding genes experienced positive selection between the two groups. Phylogenetic analyses revealed that Ziziphus (Rhamnaceae) was sister to Elaeagnaceae, and the four species of Ziziphus were clustered into two groups (Z. jujuba and Z. acidojujuba, Z. mauritiana and Z. spina-christi). Our results provide genomic resources for intrageneric classifications of Ziziphus, and valuable genetic markers for investigating the population genetics and biogeography of closely related Ziziphus species.
| S-EPMC5748658 | biostudies-literature
Project description:Indigofera stachyodes Lindl. is a traditional medicinal plant in southwestern China. In this study, we report the complete chloroplast genome sequence of I. stachyodes, using next-generation sequencing technology. The complete chloroplast genome of I. stachyodes was 158,039 bp in length with an overall GC content 35.80%, containing a large single-copy (LSC) region of 88,772 bp, a small single-copy (SSC) region of 18,733 bp, and a pair of inverted repeats (IRs) regions of 25,267 bp. In total, there are 128 genes (83 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 tRNA genes) in the whole chloroplast genome, including 113 unique genes (78 unique PCGs, 31 unique tRNAs, and four unique rRNAs). The phylogenetic analysis indicated that I. stachyodes formed a monophyletic clade with I. tinctoria and I. linifolia, showing that they have close relationship. The complete chloroplast genome of I. stachyodes provides valuable genomic information for the phylogeny, molecular identification and sustainable utilization of this species.
| S-EPMC8920384 | biostudies-literature
Project description:Codonopsis tsinglingensis, belonging to the Campanulaceae family, is a perennial medicinal herb highly valued in Chinese traditional medicine. The complete chloroplast genome of C. tsinglingensis was sequenced using the Illumina Hiseq 4000 platform. The size of the C. tsinglingensis chloroplast genome is 170,253 bp, with an average GC content of 38.3%. This circular molecule has a typical quadripartite structure containing a large single copy (LSC) region of 85,408 bp, a small single copy (SSC) region of 8179 bp, and two inverted (IRs) repeat regions of 38,333 bp. The genome contains 138 genes, including 92 protein-coding genes, 38 transfer RNA genes (tRNA), 8 ribosomal RNA genes (rRNA). Phylogenetic analysis based on complete chloroplast genome sequences of 14 species indicates that C. tsinglingensisis closely related to Codonopsis minima in the Campanulaceae family.
| S-EPMC7707307 | biostudies-literature
Project description:Aganope is a genus in the family Fabaceae, with only 11 species. They are distributed throughout Asia and Africa. Aganope dinghuensis, a newly reported species, is native to China with a restricted distribution. We, therefore, report its complete chloroplast genome for better future conservation. The chloroplast genome of A. dinghuensis is 143,690 bp, with a GC content of 35.32%. In the genome, a pair of inverted repeat regions of 13,015 bp each, a large single-copy region of 98,824 bp, and a small single-copy region of 18,836 bp were identified. Genome annotation identified 115 genes, comprising 74 protein-coding genes, 8 ribosomal RNA genes, and 33 transfer RNA genes. Repeat analysis indicates that the chloroplast genome of A. dinghuensis contains 126 simple sequence repeats (SSR), of which the majority are A/T mononucleotides. Phylogenetic analysis revealed that A. dinghuensis is a sister to the clade that includes Indigofera tinctoria, Desmodium uncinatum, Sarcodum scandens, Wisteria brachybotrys, and Callerya nitida.
| S-EPMC7889246 | biostudies-literature
Project description:Acacia crassicarpa (Fabaceae), a nitrogen-fixing tree species, is critically important for coastal protection in southeast China. In this study, we report the complete chloroplast genome sequence of A. crassicarpa, with a length of 176,493 bp. It contains a pair of inverted repeats (IR 39,851 bp), a large single-copy region (LSC 91,869 bp), and a small single-copy region (SSC 4,922 bp). The complete genome comprises 138 genes, including 93 protein-coding genes, 37 tRNA, and 8 rRNA genes. Our phylogenetic analysis reveals that A. crassicarpa is closely related to A. podalyriifolia and A. dealbata.
| S-EPMC8266222 | biostudies-literature
Project description:Desmodium uncinatum is one of the most important legume forage which distributes in tropical and subtropical regions of the world. In our study, we obtained the complete chloroplast genome of D. uncinatum with a length of 148,853 bp, including a large single copy region of 84,019 bp, small single copy region of 18,223 bp, and a pair of inverted repeat regions of 20,672 bp. The GC content in the whole chloroplast genome of D. uncinatum is 35.16%. Among the 133 unique genes in the circular genome, 37 tRNA, 12 rRNA and 84 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 11 species, and came to the conclusion that D. uncinatum was phylogenetically closely related to the genus of Glycine and Trifolium.
| S-EPMC7954487 | biostudies-literature
Project description:Ormosia purpureiflora is endemic to China. It is named after its purple flowers. It is a small tree only up to 3 m. It has leathery leaves, racemose inflorescences. The seeds are elliptic and red in coat. It is only confined to Luofushan Provincial Nature Reserve in Huizhou of Guangdong Province. Herein, we first reported on its complete chloroplast genome sequence as genomic resource for conservation purposes. The chloroplast genome of O. purpureiflora was 173,364 bp in length, with a large single-copy region of 73,465 bp, a small single-copy region of 18,751 bp, and a pair of inverted repeat regions that were 40,574 bp each. A total of 90 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes were predicted, while 106 simple sequence repeats were recorded throughout the genome. Phylogenetic analysis revealed that O. purpureiflora was sister to O. emarginata.
| S-EPMC8567912 | biostudies-literature
Project description:Medicago arabica (Linnaeus, 1762) Huds. is an important annual legume forage that grows in a wide range of climates, from subtropical to temperate. This study aimed to sequence the chloroplast genome of M. arabica and compare it with other legumes. In this study, we sequenced the entire chloroplast genome of M. arabica, which has 125,056 base pairs. The total GC content of the chloroplast genome of M. arabica was 34.4%. From the 110 unique genes of the circular genome, 30 tRNA genes, four rRNA genes, and 76 protein-coding genes were successfully annotated. A maximum likelihood (ML) tree was constructed using the model species and 17 species of the Medicago genus. M. arabica was shown to be phylogenetically closely related to M. polymorpha. The nucleotide diversity of the chloroplast genome may provide valuable molecular markers to study chloroplast, genetic breeding, and plant molecular evolution. These findings provide a solid foundation for future research on the molecular biology of the chloroplast.
| S-EPMC9045773 | biostudies-literature