Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of Betula chichibuensis (Betulaceae), a critically endangered limestone birch.

ABSTRACT: Betula chichibuensis is a critically endangered limestone birch confined to the Chichibu and Kitakami mountains in central and northeastern Japan, respectively. In this study, we assembled and characterized the complete chloroplast genome of B. chichibuensis. The whole chloroplast genome was 160,791 bp in length, consisting of a large single-copy (LSC) region of 89,504 bp and a small single-copy (SSC) region of 19,175 bp, separated by a pair of inverted repeat (IR) regions of 26,056 bp. It contained 133 genes, including 88 protein-coding genes (80 PCG types), 37 tRNA genes (30 tRNA types), and eight rRNA genes (four rRNA types). The overall GC content of the chloroplast genome was 36.01%. Phylogenetic analysis resolved B. chichibuensis as sister to the clade containing B. pendula.

SUBMITTER: Yoshida T

PROVIDER: S-EPMC7510759 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Development and evaluation of microsatellite markers for the critically endangered birch Betula chichibuensis (Betulaceae).

Project description:Microsatellite markers were developed and characterized for the critically endangered birch Betula chichibuensis (Betulaceae) to investigate the genetic structure of this species for conservation purposes. Sixteen microsatellite markers with di-, tri-, and tetranucleotide repeat motifs were developed and optimized using MiSeq paired-end sequencing. Of these, 14 were polymorphic, with two to five alleles per locus, in 47 individuals from two newly discovered populations of B. chichibuensis in Japan. Observed and unbiased expected heterozygosities per locus ranged from 0.000 to 0.617 and from 0.000 to 0.629, respectively. These markers were tested for cross-species amplification in B. maximowicziana, B. platyphylla var. japonica, and B. schmidtii. This set of microsatellite markers, the first developed for B. chichibuensis, will help elucidate spatial patterns of gene flow and levels of inbreeding in this species to aid its conservation.

| S-EPMC5435406 | biostudies-literature

Complete chloroplast genome sequence of Betula microphylla (Betulaceae).

Project description:Betula microphylla (Betulaceae) is a species widely distributed in Xinjiang China and in Mongolia and Siberia of Russia. In this study, we described the complete chloroplast genome of B. microphylla based on Illumina paired-end sequencing. The chloroplast genome of B. microphylla is 160,489 bp long, including two inverted repeats (IRs, 26,070 bp), separated by a large single-copy region (LSC, 89,306 bp), and a small single-copy region (SSC, 19,045 bp). The overall GC content of the whole genome is 36.1%, and the corresponding values of the LSC, SSC, and IR regions are 33.7%, 29.7%, and 42.5%. The phylogenetic analysis indicated that B. microphylla is closely related to Betula occidentalis.

| S-EPMC7510756 | biostudies-literature

The complete chloroplast genome of Betula costata (Betulaceae).

Project description:In the present study, we analyzed the complete chloroplast genome sequence of Betula costata using the Ion Torrent platform. The chloroplast genome of B. costata was found to be 160,547 bp in length, with a large single-copy (LSC) region of 89,385 bp, a small single-copy (SSC) region of 19,038 bp, and a pair of inverted repeats (IRs) of 26,062 bp each. The overall GC content of the chloroplast genome was 36.1%. It contained 132 genes, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic analysis indicated that B. costata is closely related to Betula nana and Betula pubescens.

| S-EPMC7748461 | biostudies-literature

Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae).

Project description:Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207?bp, sheltering a pair of inverted repeats (IR) of 25,402?bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103?bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum.

| S-EPMC5889905 | biostudies-literature

The complete chloroplast genome of Pterospermum kingtungense, a Critically Endangered species.

Project description:Pterospermum kingtungense (Pterospermum, Sterculiaceae) is a Critically Endangered species. In this study, we reported a complete chloroplast genome of P. kingtungense based on high-throughput sequencing data. The size of chloroplast genome was 162,929 bp, including a large single-copy region (LSC: 91,535 bp) and a small single-copy region (SSC: 20,464 bp), separated by a pair of inverted repeats (IRa and IRb: 25,465 bp). The genome encoded 126 genes in total, including 81 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the P. kingtungense chloroplast genome is 36.39%. The phylogenetic tree showed P. kingtungense clustered together with the family Sterculiaceae.

| S-EPMC7801019 | biostudies-literature

The complete chloroplast genome of critically endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and phylogenetic analysis.

Project description:Chimonobambusa hirtinoda, a threatened species, is only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used to obtain the complete chloroplast (cp) genome sequence of C. hirtinoda. The sequence was assembled and analyzed for phylogenetic and evolutionary studies. Additionally, we compared the cp genome of C. hirtinoda with previously published Chimonobambusa species. The cp genome of C. hirtinoda has a total length of 139, 561 bp and 38.90% GC content. This genome included a large single -copy (LSC) region of 83, 166 bp, a small single-copy (SSC) region of 20, 811 bp and a pair of inverted repeats of 21,792 bp each. We discovered 130 genes in the cp genome, including 85 protein-coding genes, 37 tRNA, and 8 rRNA genes. A total of 48 simple sequence repeats (SSRs) were detected. The A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained by measuring the codon usage frequency of amino acids. Furthermore, phylogenetic analysis using complete cp sequences and matK gene revealed a genetic relationship within the Chimonobambusa genus. This study reported the chloroplast genome of the C. hirtinoda.

| S-EPMC9187695 | biostudies-literature

The complete chloroplast genome sequence of Carpinus tibetana (Betulaceae).

Project description:The complete chloroplast genome of Carpinus tibetana was a circular DNA molecule of 158,762 bp in length, containing a large single copy region (LSC) of 87,825 bp and small single copy region (SSC) of 18,797 bp, which were separated by a pair of 26,071 bp and 26,069 bp inverted repeat regions (IRs). The all GC content of C. tibetana chloroplast genome was 36.47%. It encoded totally 127 genes, including 83 protein-coding genes, 35 tRNA genes and eight rRNA genes. The chloroplast genome of C. tibetana will provide useful genetic information for future conservation genetics and phylogenetic studies.

| S-EPMC7832502 | biostudies-literature

The complete chloroplast genome of a critically endangered tree species, Hopea reticulata (Dipterocarpaceae).

Project description:Hopea reticulata Tardieu is a critically endangered tree species distributed in limited regions in Thailand, Vietnam and Hainan Island of China. In this study, we reported the complete chloroplast genome sequence of H. reticulata assembled from pair-end reads generated by Illumina sequencing. The circular chloroplast genome is 151,407 bp in length and comprises a large single copy region of 84,352 bp, a small single copy region of 19,733 bp, and a pair of inverted repeats of 23,661 bp each. The complete genome encodes 129 functional genes, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome was 37.4%. Phylogenetic analysis showed that H. reticulata is sister to H. hainanensis with strong bootstrap support.

| S-EPMC7782000 | biostudies-literature

The complete chloroplast genome sequence of a critically endangered orchid Paphiopedilum gratrixianum (Orchidaceae).

Project description:Paphiopedilum gratrixianum is a critically endangered orchid with extremely small populations and of great horticulture value. We assembled and annotated the complete chloroplast genome of P. gratrixianum in this study. The genome is 157,292 bp in length and 35.8% of the GC content. It encodes a total of 102 unique genes, including 68 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis results strongly supported that it was closely related to P. tranlienianum. The complete chloroplast genome of P. gratrixianum (GenBank accession number: MW284890) can be useful for the evolutionary study in Orchidaceae.

| S-EPMC8979525 | biostudies-literature

The complete chloroplast genome of Pinus squamata (Pinaceae), a critically endangered species in China.

Project description:The complete chloroplast (cp) genome of Pinus squamata, a critically endangered species in China, was reported in this study. The cp genome is 118,300?bp in length and has four regions: 65,298?bp of large single copy (LSC) region and 52,098?bp of small single copy (SSC) region separated by 452?bp of highly reduced inverted repeat (IR) regions. This cp genome with GC content of 38.8% contains 107 unique genes (73 protein-coding genes, 30 tRNA genes, and four rRNA genes). Phylogenetic analysis based on the complete cp genomes indicates that P. squamata is closer to P. gerardiana than P. bungeana.

| S-EPMC7706991 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data