Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the chloroplast genome of Lagerstroemia villosa Wall. ex Kurz. (Lagerstroemia, Lythraceae).

ABSTRACT: Lagerstroemia villosa is a kind of ornamental tree with surprising potential for applying in the landscape. We characterized the complete chloroplast genome of this scarce species and analyzed its phylogeny within Lythraceae. The result showed that the genome possessed a typical quadripartite structure, in more detail, a lager single-copy region (LSC, 88,702bp), a small single-copy region (SSC, 18,255bp), and a pair of inverted repeat regions (IRa and IRb, 26,906 bp). 78 protein-coding genes, four ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes were detected. Phylogenetic analysis based on maximum likelihood (ML) supported the closest relationship between L. villosa and Lagerstroemia limii plus Lagerstroemia subcostata.

SUBMITTER: Wang J

PROVIDER: S-EPMC7801044 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae).

Project description:BackgroundCrape myrtles, belonging to the genus Lagerstroemia L., have beautiful paniculate inflorescences and are cultivated as important ornamental tree species for landscaping and gardening. However, the phylogenetic relationships within Lagerstroemia have remained unresolved likely caused by limited sampling and the insufficient number of informative sites used in previous studies.ResultsIn this study, we sequenced 20 Lagerstroemia chloroplast genomes and combined with 15 existing chloroplast genomes from the genus to investigate the phylogenetic relationships and divergence times within Lagerstroemia. The phylogenetic results indicated that this genus is a monophyletic group containing four clades. Our dating analysis suggested that Lagerstroemia originated in the late Paleocene (~ 60 Ma) and started to diversify in the middle Miocene. The diversification of most species occurred during the Pleistocene. Four variable loci, trnD-trnY-trnE, rrn16-trnI, ndhF-rpl32-trnL and ycf1, were discovered in the Lagerstroemia chloroplast genomes.ConclusionsThe chloroplast genome information was successfully utilized for molecular characterization of diverse crape myrtle samples. Our results are valuable for the global genetic diversity assessment, conservation and utilization of Lagerstroemia.

| S-EPMC8191006 | biostudies-literature

The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae).

Project description:Lagerstroemia (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for Lagerstroemia are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete plastid genome of Lagerstroemia fauriei. To our knowledge, this is the first reported whole plastid genome within Lythraceae. This genome is 152,440 bp in length with 38% GC content and consists of two single-copy regions separated by a pair of 25,793 bp inverted repeats. The large single copy and the small single copy regions span 83,921 bp and 16,933 bp, respectively. The genome contains 129 genes, including 17 located in each inverted repeat. Phylogenetic analysis of genera sampled from Geraniaceae, Myrtaceae, and Onagraceae corroborated the sister relationship between Lythraceae and Onagraceae. The plastid genomes of L. fauriei and several other Lythraceae species lack the rpl2 intron, which indicating an early loss of this intron within the Lythraceae lineage. The plastid genome of L. fauriei provides a much needed genetic resource for further phylogenetic research in Lagerstroemia and Lythraceae. Highly variable markers were identified for application in phylogenetic, barcoding and conservation genetic applications.

| S-EPMC4780714 | biostudies-literature

The complete chloroplast genome of Lagerstroemia loudonii Teijsm. & Binn. (Lythraceae), an ornamental tree with medicinal value.

Project description:Lagerstroemia loudonii is an ornamental tree with medicinal value. Here, we announce the first complete chloroplast genome sequence of L. loudonii. The L. loudonii chloroplast genome harbors a typical quadripartite structure with a total length of 152,372 bp, including a large single-copy (LSC) region of 84,086 bp, a small single-copy (SSC) region of 16,798 bp, and two separated inverted repeat (IR) regions of 25,744 bp each. The chloroplast genome encodes 130 genes, including 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The GC content of the whole chloroplast genome is 37.6%. Phylogenetic analysis based on complete chloroplast genomes of L. loudonii and 17 other plant species revealed that Lagerstroemia is a separate genus, and L. loudonii is closely related to L. calyculata.

| S-EPMC9262357 | biostudies-literature

Chloroplast Genome Sequence of Lagerstroemia guilinensis (Lythraceae, Myrtales), a Species Endemic to the Guilin Limestone Area in Guangxi Province, China.

Project description:We announce here the first complete chloroplast genome sequence of Lagerstroemia guilinensis (Lythraceae, Myrtales), a species endemic to the Guilin limestone area, along with its genome structure and functional gene annotations. The plant was collected from Guilin, Guangxi, China, and deposited as a germplasm accession of the Zhejiang Agriculture and Forestry University Collection (ZAFU 1507144). This genome will provide valuable information for future research of the Lagerstroemia genus and its relatives.

| S-EPMC4889003 | biostudies-literature

Characterization of the complete chloroplast genome of Leucomeris decora Kurz (Asteraceae).

Project description:Leucomeris decora is a traditional medicinal plant that is listed as an endangered species in China. Recently, L. decora has become locally rare. Here the complete chloroplast genome of L. decora was assembled and reported for the first time. Its plastome was 151,491 bp in length, including a large single-copy region (LSC; 83,155 bp), a small single-copy region (SSC; 18,216 bp), and a pair of inverted repeated regions (IRa and IRb; 25,060 bp). The overall GC content was 37.8%, and the genome contains 134 genes, including 92 protein-coding genes, 8 rRNA genes, and 34 tRNA genes. Phylogenetic analysis of thirteen representative species from the family of Asteraceae showed that L. decora is clustered into one clade with Gerbera jamesonii with high bootstrap values, indicating a close relationship between these two species.

| S-EPMC8725922 | biostudies-literature

Development of microsatellite markers for Lagerstroemia indica (Lythraceae) and related species.

Project description:UNLABELLED: PREMISE OF THE STUDY:Microsatellite markers were developed and characterized to analyze genetic diversity within Lagerstroemia cultivars and related species. • METHODS AND RESULTS:Using simple sequence repeat (SSR)-enriched libraries, 11 species-specific polymorphic genomic SSRs were developed from L. indica 'Hong Die Fei Wu'. All primers were tested on 48 L. indica individuals from China, the United States, and France. The primers amplified four to 12 alleles per locus, including di-, tri-, and tetranucleotide repeats. Observed and expected heterozygosities ranged from 0.1875 to 0.7609 and 0.2836 to 0.8385, respectively. The primers were also highly cross-transferrable to L. subcostata, L. limii, L. fauriei, L. caudata, and L. speciosa. • CONCLUSIONS:The new primers will enlarge the bank of SSRs available to genetic research of Lagerstroemia. These SSR markers will facilitate population genetics and molecular marker-assisted selection of L. indica.

| S-EPMC4105366 | biostudies-literature

Chloroplast genome of Trapa bispinosa Roxb. (Trapa, Lythraceae).

Project description:Trapa bispinosa Roxb. is an annual aquatic herb with great significance of medicinal, edible and economic value. Here, we reported the complete chloroplast genome sequence of Trapa bispinosa and conducted preliminary investigation of its phylogenetic relationship with other related species. As the result showed, the whole chloroplast genome size was 155,556 bp consisting of four adjoining regions, i.e., a large/small single copy (LSC, 88,506 bp/SSC, 18,274 bp) region and two inverted repeat (IRs, 24,388 bp) regions. Among 112 identified unique genes were 78 protein coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Trapa spp. were precisely clustered as a monophyly, and simultaneously, the closest relation between Trapa bispinosa and Trapa natans were strongly supported in the maximum likelihood analysis.

| S-EPMC7872573 | biostudies-literature

The complete chloroplast genome sequences of Trapa acornis Nakano (Lythraceae).

Project description:Trapa L. (Lythraceae), also called water chestnut, is a genus widely distributed in the Old World. With the high edible and medical values, the water chestnut has been cultivated popularly in China since the Tang and Song Dynasties. Among all cultivars, T. acornis Nakano is one of the most current commercial one, which grown in Jiaxing, Zhejiang province, China. However, due to the limited availability of molecular marker resources of T. acornis, we still have difficulty in its identification and utilization. Here, we reported the complete chloroplast genome sequence of T. acornis. The result demonstrated that the chloroplast genome was 155,538 bp in length, consisting of a small single copy (SSC) region of 18,275 bp, a large single copy (LSC) region of 88,492 bp, and two inverted repeat (IR) regions of 24,386 bp. The chloroplast genome contains a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenomic analysis demonstrated the sister relationship between T. acornis and T. bicornis.

| S-EPMC8667907 | biostudies-literature

Complete chloroplast genome of medicinal plant Sabia parviflora Wall. ex Roxb. (Sabiaceae).

Project description:Sabia parviflora Wall. ex Roxb., an evergreen climbing woody vine, is a Chinese herbal medicine commonly used by ethnic minorities in some areas of China. In this study, the chloroplast genome of S. parviflora was sequenced for the first time. Its genome is 162,054 bp in length with 38.6% of GC content. The genome consists of a large single copy (LSC) region of 90,001 bp, a small single copy (SSC) region of 18,887 bp, and two inverted repeat (IRa and IRb) regions of 26,583 bp each. A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis was conducted by nine species from order Proteales, which demonstrated a close relationship between the family Sabiaceae and Nelumbonaceae.

| S-EPMC8189099 | biostudies-literature

The complete chloroplast genome sequence of Trapa bicornis Osbeck (Lythraceae).

Project description:Trapa (Lythraceae) is an aquatic plant genus widely distributed in the old world. Although Trapa species have great edible and medical value, studies related to species identification and utilization are still lacking. Here, we reported the complete chloroplast genome sequence of a cultivated species, T. bicornis. The chloroplast genome size of T. bicornis was 155,539 bp, consisting of a pair of inverted repeat (IR) regions (24,386 bp), separated by a large single copy (LSC) region (88,493 bp) and a small single copy (SSC) region (18,274 bp). A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenomic analysis supported the monophyly of Trapa, and a sister relationship between T. bicornis and T. natans.

| S-EPMC7782891 | 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