Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Gu C

PROVIDER: S-EPMC4889003 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Gu Cuihua C Tembrock Luke R LR Wu Zhiqiang Z

Genome announcements 20160519 3

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 it ...[more]

PMID: 27198012

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

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

Project description: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.

| S-EPMC7801044 | biostudies-literature

Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales.

Project description:BackgroundLythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45; Nesaea, with 50; Lagerstroemia, with 56; and Cuphea, with 275 species.ResultsWe reported six newly sequenced chloroplast (cp) genomes (Duabanga grandiflora, Trapa natans, Lythrum salicaria, Lawsonia inermis, Woodfordia fruticosa and Rotala rotundifolia) and compared them with 16 other cp genomes of Lythraceae species. The cp genomes of the 22 Lythraceae species ranged in length from 152,049 bp to 160,769 bp. In each Lythraceae species, the cp genome contained 112 genes consisting of 78 protein coding genes, four ribosomal RNAs and 30 transfer RNAs. Furthermore, we detected 211-332 simple sequence repeats (SSRs) in six categories and 7-27 long repeats in four categories. We selected ten divergent hotspots (ndhF, matK, ycf1, rpl22, rpl32, trnK-rps16, trnR-atpA, rpl32-trnL, trnH-psbA and trnG-trnR) among the 22 Lythraceae species to be potential molecular markers. We constructed phylogenetic trees from 42 Myrtales plants with 8 Geraniales plants as out groups. The relationships among the Myrtales species were effectively distinguished by maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) trees constructed using 66 protein coding genes. Generally, the 22 Lythraceae species gathered into one clade, which was resolved as sister to the three Onagraceae species. Compared with Melastomataceae and Myrtaceae, Lythraceae and Onagraceae differentiated later within Myrtales.ConclusionsThe study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study.

| S-EPMC6595698 | biostudies-literature

The complete chloroplast genome of Hemiboea pterocaulis (Gesneriaceae) exclusively distributed in Guilin, Guangxi, China.

Project description:Hemiboea pterocaulis is a unique species only found in Guilin, Guangxi, China. In this study, we sequenced and assembled the complete chloroplast genome of H. pterocaulis and revealed its phylogenetic relationship with other Hemiboea species. The chloroplast genome sequence of H. pterocaulis is 153,159 bp in length and comprises a large single-copy (LSC) region of 84,178 bp, a small single-copy (SSC) region of 18,087 bp, and a pair of inverted repeat (IR) regions, each with a length of 25,447 bp. It has a total GC content of 37.6% and encodes 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic relationships based on the complete chloroplast genome sequences of Hemiboea taxa indicate that H. pterocaulis is most closely related to H. suiyangensis, indicating that H. pterocaulis is an independent species and is separated from the H. subcapitata complex. These results provide valuable insights into the phylogeny, species divergence, and delimitation of the Hemiboea genus.

| S-EPMC10984237 | 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

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

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

Lysimachia fanii, a new species of Primulaceae from limestone area of Guangxi, China.

Project description:Lysimachia fanii, a new species of Lysimachia (Subgen. Idiophyton, Primulaceae), is described and illustrated from Guangxi, China based on morphological and molecular data. Lysimachia fanii differs from L. verbascifolia, L. rupestris and L. alpestris mainly by the habit being nearly rosulate, leaves congested at the apex of the rhizome, leaf blades spatulate to narrowly oblanceolate and flowers solitary. Phylogenetic analyses supported L. verbascifolia as sister to L. fanii. This new species is endemic to limestone areas in Liucheng county of Guangxi, China.

| S-EPMC6728382 | biostudies-literature

Lysimachia xiangxiensis (Primulaceae), a new species from limestone area in Hunan Province, central China.

Project description:A new species of Lysimachia, L. xiangxiensis (Primulaceae), is described and illustrated from western Hunan, central China. The species is similar to L. melampyroides in plant densely strigillose, leaves subglabrous adaxially, and flowers usually solitary in axils of upper leaves, but differs by the succulent leaves, the creeping or ascending stems 15-25 cm long, and the suborbicular to broadly elliptic corolla lobes. This new species is also supported by a molecular phylogenetic analysis of some Lysimachia species based on ITS sequence data.

| S-EPMC7052036 | biostudies-literature

Primulinasilaniae sp. nov. (Gesneriaceae) from the limestone area of Guizhou Province, China.

Project description:Primulinasilaniae X.X.Bai & F.Wen, a new species of Primulina Hance (Gesneriaceae) from the limestone area of Wangmo County, Guizhou Province, is described and illustrated. The new species is similar to P.spiradiclioides Z.B.Xin & F.Wen, but can be easily distinguished from the latter by a combination of characteristics, especially in the lateral veins of its leaf and floral shape and tube. At present, three populations in one locality of this new taxon were found, totaling about 600 mature individuals. According to the IUCN Red List Categories and Criteria (Version 3.1), the species is provisionally assessed as Vulnerable [VU D1].

| S-EPMC8642359 | 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