Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromosome level genome assembly of endangered medicinal plant Anisodus tanguticus.

ABSTRACT: Anisodus tanguticus is a medicinal herb that belongs to the Anisodus genus of the Solanaceae family. This endangered herb is mainly distributed in Qinghai-Tibet Plateau. In this study, we combined the Illumina short-read, Nanopore long-read and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to de novo assemble the A. tanguticus genome. A high-quality chromosomal-level genome assembly was obtained with a genome size of 1.26 Gb and a contig N50 of 25.07 Mb. Of the draft genome sequences, 97.47% were anchored to 24 pseudochromosomes with a scaffold N50 of 51.28 Mb. In addition, 842.14 Mb of transposable elements occupying 66.70% of the genome assembly were identified and 44,252 protein-coding genes were predicted. The genome assembly of A. tanguticus will provide genetic repertoire to understand the adaptation strategy of Anisodus species in the plateau, which will further promote the conservation of endangered A. tanguticus resources.

SUBMITTER: Song Y

PROVIDER: S-EPMC10837431 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Chromosome level genome assembly of endangered medicinal plant Anisodus tanguticus.

Song Yongli Y Huang Jian-Ping JP Wang Yong-Jiang YJ Huang Sheng-Xiong SX

Scientific data 20240202 1

Anisodus tanguticus is a medicinal herb that belongs to the Anisodus genus of the Solanaceae family. This endangered herb is mainly distributed in Qinghai-Tibet Plateau. In this study, we combined the Illumina short-read, Nanopore long-read and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to de novo assemble the A. tanguticus genome. A high-quality chromosomal-level genome assembly was obtained with a genome size of 1.26 Gb and a contig N50 of 25.07 Mb. Of the d ...[more]

PMID: 38307894

Similar Datasets

Chromosome-level genome assembly of the endangered plant Tetraena mongolica.

Project description:Tetraena mongolica is an endangered xerophytic shrub with high ecological value for the restoration of desert vegetation because of its high tolerance to drought and heat stress. Here, we generated a high-quality chromosome-level reference genome of T. mongolica by combining PacBio HiFi data and Hi-C sequencing technologies, which was approximately 1.12 Gb (contig N50 of 25.5 Mb) in size and contained 61,888 protein-coding genes; repetitive sequences comprised 44.8% of the genome. This genome of T. mongolica is the first published genome sequence of a member of the order Zygophyllales. Genome analysis showed that T. mongolica has undergone a recent whole genome duplication event, and a recent burst of long terminal repeat insertions afterward, which may be responsible for its genome size expansion and drought adaptation. We also conducted searches for gene homologues and identified terpene synthase (TPS) gene families and candidate genes involved in triacylglycerol biosynthesis. The T. mongolica genome sequence could aid future studies aimed at functional gene identification, germplasm resource management, molecular breeding efforts, as well as evolutionary studies of Fabids and angiosperm taxa.

| S-EPMC10113878 | biostudies-literature

A Chromosome-level genome assembly of the alpine medicinal plant Bergenia purpurascens (Saxifragaceae).

Project description:Mountain ecosystems harbor high levels of biodiversity, but the genetic mechanisms underlying adaptation to harsh alpine conditions remain largely unknown. Bergenia purpurascens (Saxifragaceae) is an important alpine endemic species of the Himalaya-Hengduan Mountains (HHM), with this species being used as a source of medicine and as an ornamental plant. In this study, we generated a high-quality genome assembly comprising scaffolds representing the 17 chromosomes, with a total length of 650.70 Mb and a scaffold N50 of 34.19 Mb. A total of 45,841 protein-coding genes were annotated, and 10,797 noncoding RNAs were identified. Repeat sequences accounted for 56.72% of the genome. The reference genome of B. purpurascens serves as a valuable resource for studying bergenin biosynthesis, and understanding adaptation of plants to alpine environments.

| S-EPMC11751328 | biostudies-literature

Chromosome-level genome assembly of an endangered plant Prunus mongolica using PacBio and Hi-C technologies.

Project description:Prunus mongolica is an ecologically and economically important xerophytic tree native to Northwest China. Here, we report a high-quality, chromosome-level P. mongolica genome assembly integrating PacBio high-fidelity sequencing and Hi-C technology. The assembled genome was 233.17 Mb in size, with 98.89% assigned to eight pseudochromosomes. The genome had contig and scaffold N50s of 24.33 Mb and 26.54 Mb, respectively, a BUSCO completeness score of 98.76%, and CEGMA indicated that 98.47% of the assembled genome was reliably annotated. The genome contained a total of 88.54 Mb (37.97%) of repetitive sequences and 23,798 protein-coding genes. We found that P. mongolica experienced two whole-genome duplications, with the most recent event occurring ~3.57 million years ago. Phylogenetic and chromosome syntenic analyses revealed that P. mongolica was closely related to P. persica and P. dulcis. Furthermore, we identified a number of candidate genes involved in drought tolerance and fatty acid biosynthesis. These candidate genes are likely to prove useful in studies of drought tolerance and fatty acid biosynthesis in P. mongolica, and will provide important genetic resources for molecular breeding and improvement experiments in Prunus species. This high-quality reference genome will also accelerate the study of the adaptation of xerophytic plants to drought.

| S-EPMC10254739 | biostudies-literature

Chromosome-Level Genome Assembly of the Rare and Endangered Tropical Plant <i>Speranskia yunnanensis</i> (Euphorbiaceae).

Project description: Not available

| S-EPMC8819086 | biostudies-literature

Chromosomal level genome assembly of medicinal plant Sophora flavescens.

Project description:Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). In this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs), which have recently and rapidly proliferated. This genome size is ~5x larger than its closest sequenced relative Lupinus albus L. . We annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues, and also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome highlights the very different evolutionary trajectories that have occurred in recently diverged Fabaceae, leading to smaller duplicated genomes.

| S-EPMC10465603 | biostudies-literature

Chromosome-scale genome assembly of an important medicinal plant honeysuckle.

Project description:Lonicera japonica (honeysuckle) is one of the most important medicinal plants and widely utilized in traditional Chinese medicine. At present, there are many varieties of honeysuckle used in cultivation, among which Sijihua variety are widely cultivated due to its wide adaptability, stress resistance, early flowering and high yield. In this study, we assembled the genome of Sijihua, which was approximately 886.04 Mb in size with a scaffold N50 of 79.5 Mb. 93.28% of the total assembled sequences were anchored to 9 pseudo-chromosomes by using PacBio long reads and Hi-C sequencing data. We predicted 39,320 protein-coding genes and 92.87% of them could be annotated in NR, GO, KOG, KEGG and other databases. In addition, we identified 644 tRNAs, 2,156 rRNAs, 109 miRNAs and 5,502 pseudogenes from the genome. The chromosome-scale genome of Sijihua will be a significant resource for understanding the genetic basis of high stress-resistance, which will facilitate further study of the genetic diversity and accelerate the genetic improvement and breeding of L. japonica.

| S-EPMC9130202 | biostudies-literature

A core root bacteria contribute to plant growth and anisodine accumulation of Anisodus tanguticus.

Project description:BackgroundAlthough it is well recognized that core root microorganisms contribute to plant health and productivity, little is known about their role to the accumulation of secondary metabolites. The roots of Anisodus tanguticus, a traditional herbal medication utilized by Tibetan medicine, are rich in tropane alkaloids. We collected wild A. tanguticus populations throughout a 1500 km transect on the Qinghai-Tibetan Plateau.ResultsOur results showed that despite sampling at a distance of 1500 km, the root of A. tanguticus selectively recruits core root bacteria. We obtained 102 root bacterial core OTUs, and although their number only accounted for 2.99% of the total, their relative abundance accounted for 73% of the total. Spearman correlation and random forest analyses revealed that the composition of core root microbiomes was related to anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. Among them, the main role is played by Rhizobacter, Variovorax, Polaromonas, and Mycobacterium genus that are significantly enriched in roots. Functional prediction by FAPROTAX showed that nitrogen-cycling microorganisms and pathogenic bacteria are strongly associated with anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus.ConclusionsOur findings show that the root selectively recruits core root bacteria and revealed that the core microbiomes and microbial functions potentially contributed to the anisodine contents, aboveground biomass and nitrogen contents of the plant. This work may increase our understanding of the interactions between microorganisms and plants and improve our ability to manage root microbiota to promote sustainable production of herbal medicines.

| S-EPMC10729362 | biostudies-literature