Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of China Lindera praecox (Lauraceae) and intra-species diversity.

ABSTRACT: Lindera praecox is a signature composition in the broadleaved deciduous forest of East China and Japan. Presently, the complete chloroplast (cp) genome of this species was sequenced, assembled, and annotated. It is 152,818 bp in length and encodes 85 protein-coding genes, 36 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated intraspecific varieties within L. praecox species collected in China and Japan. This chloroplast genome sequencing offers genetic background for resources conservation and phylogenetic studies.

SUBMITTER: Yu J

PROVIDER: S-EPMC8253210 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae).

Project description:Lindera, a core genus of the Lauraceae family, has important economic uses in eastern Asia and North America. However, its historical diversification has not been clarified. In this study, we report nine newly sequenced Lindera plastomes. The plastomes of these nine Lindera species range from 152,211 (L. nacusua) to 152,968 bp (L. metcalfiana) in length, similar to that of another Lauraceae species, Litsea glutinosa (152,618 bp). The length variation of these plastomes derived from the length variation in the loci ycf1, ycf2, ψycf1, and ndhF-ψycf1. Comparing our sequences with other available plastomes in the Lauraceae indicated that eight hypervariable loci, ihbA-trnG, ndhA, ndhF-rpl32, petA-psbJ, psbK-psbI, rps16, trnS-trnG, and ycf1, could serve as DNA barcodes for species delineation, and that the inverted repeats (IRs) showed contraction/expansion. Further phylogenetic analyses were performed using 32 complete plastomes of Lauraceae and seven barcodes from 14 additional species of Lindera and related species in the core Lauraceae. The results showed that these Lindera species grouped into two or four sub-clades, and that two Litsea species and Laurus nobilis were located in the same sub-clade as five Lindera species. These data support a close relationship between the genera Laurus, Lindera, and Litsea, and suggest that Lindera is polyphyletic.

| S-EPMC5995902 | biostudies-literature

The complete chloroplast genome sequence of Lindera fragrans (Lauraceae): genome structure and phylogenetic analysis.

Project description:Lindera fragrans, naturally distributed in southern China, is economic and ecological tree. Its leaves are one of the primary raw materials for processing Hawk tea. Here, we assembled the complete chloroplast genome of L. fragrans using Illumina pair-end sequencing. The chloroplast genome size was 152,739 base pairs (bp) with 39% GC content, containing a pair of inverted repeats (IRA/B) of 20,067 bp, separated by a large- and a small single-copy region (LSC/SSC) of 93,711 bp and 18,894 bp, respectively. The genome encoded 126 genes, including 82 protein-coding, 36 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis based on chloroplast genome sequences of 22 species suggested that L. fragrans was closely related to species of Lindera genus than other genera in Lauraceae. These results can be a valuable genome resource for further genetics and molecular biology studies.

| S-EPMC9248934 | biostudies-literature

Characterization of two complete chloroplast genomes of Lindera megaphylla (Lauraceae).

Project description:Lindera megaphylla (Lauraceae) is an ecologically important and dominant evergreen broad-leaf tree species in the warm-temperate and subtropical zone of China. In this study, we sequenced and assembled two complete genomes of L. megaphylla (LM01 and LM02) based on the next-generation sequencing data. The two complete chloroplasts of L. megaphylla are 152,741 bp in length, including two same length inverted repeats of 20,067 and 20,068 bp, a small single copy of 18,882 and 18,914 bp and a large single copy of 93,726 and 93,691 bp for LM01 and LM02 respectively. They all contain 84 protein-coding, 36 tRNA and eight rRNA genes. The phylogenetic analysis based on chloroplast genomes indicates that L. megaphylla is closely related to another Lindera and Litsea species.

| S-EPMC7706839 | biostudies-literature

Complete chloroplast genome sequence of Chimonanthus praecox link (Calycanthaceae): an endemic plant species in China.

Project description:Chimonanthus praecox, a deciduous shrub tree, is endemic to China and widely cultivated in the world as a popular garden and ornamental plant. Here, we have reported its complete chloroplast genome with a length of 153,181 bp, containing a large single copy (LSC) region of 86,916 bp, a small single copy (SSC) region of 19,767 bp and two identical inverted repeat regions (IRs) of 23,249 bp. The overall GC contents of the plastome were 39.27%. A total of 114 unique genes were successfully annotated consisting of 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Sixteen genes each possessed one intron and three genes had two introns. The ML phylogenetic analysis supports Chimonanthus as sister to Calycanthus. This result will be helpful for genetic breeding and population genetics of C. praecox, DNA barcoding of Chimonanthus, and phylogenetic studies of Calycanthaceae.

| S-EPMC7782217 | biostudies-literature

The complete chloroplast genome of Lindera pulcherrima var. hemsleyana (Lauraceae).

Project description:Lindera pulcherrima var. hemsleyana is an evergreen tree of the genus Lindera with important medicinal value. The complete chloroplast genome of L. pulcherrima var. hemsleyana is 152,710 bp in length, containing a LSC region of 93,751 bp, a SSC region of 18,813 bp, and a pair of inverted repeats (IRA and IRB) of 20,073 bp each. The genome encoded 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, 36 transfer RNA genes, and one pseudogene (ycf1). Most of these genes occurred in a single copy, whereas 15 genes occurred in double copies, including all rRNA, 6 tRNA, and 5 protein-coding genes. The GC content of the whole genome, LSC, SSC, and IR regions is 39.2%, 38.0%, 33.9%, and 44.4%, respectively. A total of 90 SSRs were discovered, the numbers of mono-, di-, tri-, tetra-, penta-, and hexa-nucleotides SSRs were 66, 10, 4, 8, 1, and 1, respectively. Phylogenetic analysis of cp genomes from 24 species of Lauraceae revealed that cp genomes of L. pulcherrima var. hemsleyana, L. pulcherrima var. attenuata, and L. pulcherrima formed a monophyletic clade with 100% bootstrap value.

| S-EPMC7782348 | biostudies-literature

The complete chloroplast genome sequence of Korean Lonicera japonica and intra-species diversity.

Project description:Lonicera japonica is a traditional medicinal plant well known for its anti-inflammatory effect. The complete chloroplast genome sequence of L. japonica collected from Korea was obtained by de novo assembly using whole genome sequence data. The chloroplast genome is 155,060?bp in length, containing 88,853?bp in a large single copy (LSC), 18,653?bp in a small single copy (SSC) and 23,777?bp in a pair of inverted repeats (IRs). A total of 112 genes including 78 protein-coding genes and 34 structural RNA genes were identified. The sequence comparison of two L. japonica collected from Korea and China revealed 48 single nucleotide polymorphisms (SNPs) and 45 insertions/deletions (InDels). In addition, phylogenetic analysis represented intraspecific diversity within L. japonica species collected in Korea and China.

| S-EPMC7800441 | biostudies-literature

Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species.

Project description:BACKGROUND:Phoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus. RESULTS:We sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies. CONCLUSION:This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

| S-EPMC5597560 | biostudies-literature

Development of 20 chloroplast microsatellite primers in wuyao (Lindera aggregata, Lauraceae).

Project description:Premise of the studyTo investigate the population genetics and evolutionary history of wuyao (Lindera aggregata, Lauraceae) and other Lindera species, polymorphic chloroplast microsatellite (cpSSR) primers were developed.Methods and resultsThe complete chloroplast genome of L. glauca was used to design 74 primers for L. aggregata. Agarose gel electrophoresis and Sanger sequencing were used to select 20 polymorphic primers. These primers were then tested in 70 individuals from three populations of L. aggregata. The number of alleles ranged from two to four, and the unbiased haploid diversity index ranged from 0.457 to 0.685. Up to 17 primers successfully amplified in four other Lindera species: L. prattii, L. chunii, L. lungshengensis, and L. pulcherrima var. hemsleyana.ConclusionsThe 20 primers reported here can potentially be used for future genetic studies of L. aggregata and other Lindera species.

| S-EPMC6711346 | biostudies-literature

Characterization of the complete chloroplast genome of China Viburnum burejaeticum Regel et Herd and intra-species diversity.

Project description:Viburnum burejaeticum Regel et Herd is widely cultivated in botanical gardens. However, as a member of Adoxaceae, few studies have been carried out on its phylogenetic relationship with other family members. Here we report the first complete chloroplast (cp) genome sequence of V. burejaeticum collected from China. The circular cp genome is 158,381 bp in size, including a large single-copy (LSC) region of 87,067 bp and a small single-copy (SSC) region of 18,212 bp, which were separated by two inverted repeat (IR) regions (26,551 bp each). A total of 126 genes were annotated, including 8 ribosomal RNAs (rRNAs), 36 transfer RNAs (tRNAs), and 82 protein-coding genes (PCGs). The sequence comparison of two V. burejaeticum collected from Korea and China revealed 101 single nucleotide polymorphisms (SNPs) and 16 insertions/deletions (InDels). In addition, maximum-likelihood (ML) phylogenetic analysis indicated V. burejaeticum species collected in Korea and China are clustered together. This study provides useful information for future genetic study of V. burejaeticum.

| S-EPMC8032331 | biostudies-literature

Complete chloroplast genome sequence and annotation of Machilus salicina Hance, 1885 (lauraceae)

Project description:Abstract Machilus salicina Hance, 1885 is a species of flowering plant in the family Lauraceae and is mainly found at low altitudes in southern China. In this study, we assembled and annotated the complete chloroplast genome of M. salicina for the first time. We analyzed the general features of M. salicina and constructed a phylogenetic tree based on 15 Lauraceae species. The chloroplast genome of M. salicina had a total length of 153,943 bp. The length of a large single copy region, a small single copy region, and two inverted repeat regions were 93,689 bp, 20,070 bp, and 20,092bp, respectively. A total of 128 genes were detected, which included 84 protein-coding genes, 36 tRNAs and 8 rRNAs. The GC content of M. salicina complete chloroplast genome was 39.1%. The phylogenetic tree indicated that M. salicina was closely related to M. yunnanensis.

| S-EPMC9090370 | 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