Complete chloroplast genome of the rare medicinal vegetable Allium hookeri.
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ABSTRACT:
SUBMITTER: Ren F
PROVIDER: S-EPMC8667927 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Schnabelia tetrodonta is a medicinal plant used in traditional Chinese medicine. However, the molecular biology data of the species was too scarce to bioprospect the medicinal species. In this study, the first complete chloroplast genome (cp) of S. tetrodonta was sequenced and assembled based on the next generation sequencing. The cp genome is 157,004 bp in length, including a large single-copy (LSC) region of 83,605 bp, a small single-copy (SSC) region of 36,899 bp, and a pair of inverted repeat (IR) regions of 18,250 bp each. The genome encodes 134 genes, including 90 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The GC content of whole genome is 37.80%. The phylogenetic analysis based on 20 complete cp sequences (19 genome sequences from the Teucrioideae of Lamiaceae and an outgroup of Ipomoea purpurea) revealed that S. tetrodonta was closely related to S. oligophylla.
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Project description:The genus Allium is one of the world's largest monocot genera. However, few reports on the complete chloroplast genome of Allium plants are reported. In this study, we reported the complete chloroplast genome of Allium prattii. The genome sequence was 154,482?bp in length, including a large single copy region (LSC) of 83,392?bp and a small single copy region (SSC) of 18,064?bp, which were separated by two inverted repeat (IR) regions of 26,513?bp. The complete chloroplast genome contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with several reported chloroplast genomes showed that A. prattii has a close genetic relationship with A. cepa and A. sativum.
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Project description:Allium tuberosum is a popular vegetable, condiment, and even a traditional Chinese medicine. Here, the complete chloroplast genome sequence of Allium tuberosum was reported. The size of the chloroplast genome is 154,056 bp in length, including a large single copy region (LSC) of 83,068 bp, a small single copy region (SSC) of 17,958 bp, and a pair of inverted repeat (IR) regions with 26,515 bp. The Allium tuberosum chloroplast genome encodes 132 genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic tree analysis suggested that Allium tuberosum was closely related to Allium sativum.
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Project description:Allium mongolicum is a kind of wild vegetable with high nutritional value and even a traditional Chinese medicine. Here, we reported the complete chloroplast genome sequence of Allium mongolicum. The size of the chloroplast genome is 153,376 bp in length, including a large single copy region (LSC) of 82,912 bp, a small single copy region (SSC) of 18,054 bp, and a pair of inverted repeated regions of 26,205 bp. The Allium mongolicum chloroplast genome encodes 115 genes, including 69 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that Allium mongolicum is closely related to Allium przewalskianum.
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Project description:The genus Allium is one of the largest monocotyledonous genera, containing over 850 species, and most of these species are found in temperate climates of the Northern Hemisphere. Furthermore, as a large number of new Allium species continue to be identified, phylogenetic classification based on morphological characteristics and a few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present the use of complete chloroplast genome sequences in genome-scale phylogenetic studies of Allium. We sequenced and assembled four Allium chloroplast genomes and retrieved five published chloroplast genomes from GenBank. All nine chloroplast genomes were used for genomic comparison and phylogenetic inference. The chloroplast genomes, ranging from 152,387 bp to 154,482 bp in length, exhibited conservation of genomic structure, and gene organization and order. Subsequently, we observed the expansion of IRs from the basal monocot Acorus americanus to Allium, identified 814 simple sequence repeats, 131 tandem repeats, 154 dispersed repeats and 109 palindromic repeats, and found six highly variable regions. The phylogenetic relationships of the Allium species inferred from the chloroplast genomes obtained high support, indicating that chloroplast genome data will be useful for further resolution of the phylogeny of the genus Allium.
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Project description:Pogostemon cablin, the natural source of patchouli alcohol, is an important herb in the Lamiaceae family. Here, we present the entire chloroplast genome of P. cablin. This genome, with 38.24% GC content, is 152,460 bp in length. The genome presents a typical quadripartite structure with two inverted repeats (each 25,417 bp in length), separated by one small and one large single-copy region (17,652 and 83,974 bp in length, respectively). The chloroplast genome encodes 127 genes, of which 107 genes are single-copy, including 79 protein-coding genes, four rRNA genes, and 24 tRNA genes. The genome structure, GC content, and codon usage of this chloroplast genome are similar to those of other species in the family, except that it encodes less protein-coding genes and tRNA genes. Phylogenetic analysis reveals that P. cablin diverged from the Scutellarioideae clade about 29.45 million years ago (Mya). Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to high AT content in the chloroplast genome. Complete sequences and annotation of P. cablin chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.
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Project description:Sophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.
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