Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Lithocarpus longinux (Fagaceae).

ABSTRACT: Lithocarpus longinux (Hu) Chun ex Y.C.Hsu & H.Wei Jen is a Critically Endangered tree distributed in Ma-li-po county in the Southeastern Yunnan Province China. Less than ten individuals have been found since the species was established 70 years ago. In this study, we assembled and annotated the complete chloroplast genome of L. longinux. The complete chloroplast genome of the species is 161,420 bp in length and has a GC content of 36.8%, including one large single-copy region (LSC, 90,409 bp), one small single-copy region (SSC, 19,255 bp), and two copies of inverted repeat regions (IRs, 25,878 bp). A total of 112 unique genes were detected, including 81 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Phylogenetic analysis of 31 representative chloroplast genomes of the Fagales suggests Lithocarpus is monophyletic with strong bootstrap support and that L. longinux is closely related to L. balansae.

SUBMITTER: Wu CY

PROVIDER: S-EPMC9262355 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Lithocarpus litseifolius (Hance) Chun 1837 (Fagaceae) and phylogenetic analysis.

Project description:Lithocarpus litseifolius (Hance) Chun 1837 is an evergreen tree of Fagaceae, which can be used as sweet tea, natural sweetener, and precious medicinal material. The complete chloroplast genome of L. litseifolius was sequenced and its phylogenetic relationship was analyzed in this study. The chloroplast genome of L. litseifolius has a circular structure with a length of 161,322 bp, and it contains a pair of inverted repeat regions (IRs 25,897 bp), a large single copy (LSC 90,551 bp), and a small single copy (SSC 18,977 bp). There were 131 genes identified, including 37 tRNA, 8 rRNA, and 86 mRNA genes. Phylogenetic analysis of 23 species of Fagaceae indicated that Lithocarpus is monophyletic with strong bootstrap, and L. litseifolius is genetically closely related to Lithocarpus polystachyus.

| S-EPMC10187088 | biostudies-literature

The complete chloroplast genome sequence of Quercus gilva?Fagaceae?.

Project description:Quercus gilva is classified as the national second-class protective tree species in China and is widely distributed in Middle East Asia. We determined the complete chloroplast genome sequence for Q. gilva using Illumina sequencing data. The complete chloroplast sequence is 160,763?bp, including large single-copy (LSC) region of 90,292?bp, small single-copy (SSC) region of 18,831?bp, and a pair of invert repeats (IR) regions of 25,820?bp. Plastid genome contains 128 genes, 80 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 26 chloroplast genomes indicates that Q. gilva is closely related to Q. sichourensis in Fagaceae.

| S-EPMC7687598 | biostudies-literature

The complete chloroplast genome sequence of Quercus phillyraeoides (Fagaceae).

Project description:Quercus phillyraeoides A. Gray is an evergreen oak species native to East Asia, and it plays a vital role in mountain ecosystems. In this study, we assembled the complete chloroplast genome of Q. phillyraeoides based on sequencing data. The genome was circular and 161,384 bp in length, consisting of a large single-copy region (90,617 bp), small single-copy region (19,035 bp), and two short inverted repeat regions (25,866 bp). We found that the cp genome encodes for 131 genes, including 85 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The results of the phylogenetic analysis of the complete cp genome sequence illustrated that Q. phillyraeoides is a member of the section Quercus and it is most closely related to Q. tarokoensis.

| S-EPMC7748451 | biostudies-literature

The complete chloroplast genome sequence of Quercus myrsinifolia (Fagaceae).

Project description:Quercus myrsinifolia Blume is an evergreen oak tree species native to East Asia, and is also one of the dominant trees of subtropical evergreen broad-leaved forests. In this study, we sequenced and analysed the complete chloroplast (cp) genome of the species. The circular genome is 160,803 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,840 bp, one large single-copy (LSC) region of 90,223 bp, and one small single-copy (SSC) region of 18,900 bp. It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 30 cp genome sequences indicated that Q. myrsinifolia was among the members of section Cyclobalanopsis, and was most closely related to Q. sichourensis.

| S-EPMC7706793 | biostudies-literature

The complete chloroplast genome sequence of Quercus franchetii Skan (Fagaceae).

Project description:Quercus franchetii Skan, a crucial indicator plant of dry-hot valley with endemic to southwestern China. In this study, the complete chloroplast genome of Q. franchetii was assembled and characterized. The circular genome was 160,785 bp in length, containing a large single copy (LSC) region of 90,169 bp, a small single copy (SSC) region of 18,828 bp, and a pair of inverted repeat regions of 25,894 bp. Total 131 genes were annotated, comprising 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that Q. franchetii was closely related to Q. glauca and Q. chungii.

| S-EPMC8451670 | biostudies-literature

The complete chloroplast genome sequence of Castanopsis fordii Hance (Fagaceae).

Project description:Castanopsis fordii Hance 1884 is a typical evergreen broad-leaved forest plant in the south subtropical and middle subtropical regions of China. It has high utilization value in wood production and soil erosion protection. Here, we first reported and characterized the complete chloroplast (cp) genome sequence of C. fordii based on Illumina paired-end sequencing data. The complete cp genome sequence of C. fordii was 160,853 base pairs (bp) in length which contained two inverted repeats (IRs) of 25,699 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 90,474 bp and 18,981 bp, respectively. The cpDNA contained 129 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes. The overall GC content of the plastome was 36.8%. Phylogenetic analysis base on 14 chloroplast genomes indicated that C. fordii was closely related to the species C. tibetana and C. concinna in Fagaceae.

| S-EPMC9930788 | biostudies-literature

The complete chloroplast genome sequence of Quercus sessilifolia Blume (Fagaceae).

Project description:Quercus sessilifolia Blume is one of the dominant tree species in East Asian evergreen broadleaved forests. In this study, we assembled and characterized the plastome of Q. sessilifolia using Illumina paired-end data. The circular genome is 160,813 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,862 bp, one large single-copy (LSC) region of 90,218 bp, and one small single-copy (SSC) region of 18,871 bp. It encodes a total of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 28 chloroplast genome sequences indicated that Q. sessilifolia was most closely related to Q. myrsinifolia with 90% bootstrap support.

| S-EPMC8751490 | biostudies-literature

The characteristic of the complete chloroplast genome of Lithocarpus konishii (Fagaceae), a rare and endemic species in South China.

Project description:Lithocarpus konishii, a rare species endemic to islands in South China, was evaluated as a vulnerable species (VU) by the 'China Species Red List.' Here, we first presented the complete chloroplast genome sequence of L. konishii. The chloroplast genome was 161,059 bp in length with 36.76% GC content, containing a small single-copy region (SSC, 18,967 bp), a large single-copy region (LSC, 90,250 bp), and a pair of inverted repeats (IRs, 25,921 bp each). A total of 139 genes were predicted, including 87 protein-coding genes (CDS), 8 rRNAs, and 44 tRNAs. Based on the concatenated shared unique CDS sequence dataset, maximum-likelihood and Bayesian inference methods were used to build the phylogenetic trees of 18 species from the Fagaceae family. Results indicated that L. konishii is closely related to L. longnux and L. pachyphyllus var. fruticosus, and forms a monophyly of the subfamily Castaneoideae with Castanopsis and Castanea. This study provides a theoretical basis for the conservation genomics of this endangered plant.

| S-EPMC10286688 | biostudies-literature

The complete chloroplast genome sequence of Castanopsis sclerophylla (Lindl.) Schott (Fagaceae).

Project description:Castanopsis sclerophylla (Lindl.) Schott is one of the National Class II protected plants, and an important species in subtropical evergreen forests in China. The object of this work was to thoroughly explore the complete chloroplast (cp) genome of C. sclerophylla using next-generation sequencing. The circular complete cp genome of C. sclerophylla is 160,519 bp in length, containing a large single-copy (LSC) region of 90,243 bp, and a small single-copy (SSC) region of 18,976 bp. It comprises 131 genes, including 8 rRNA genes, 37 tRNAs genes, and 85 protein-coding genes. The GC content of C. sclerophylla cp genome is 36.81%. The phylogenetic analysis suggests that C. sclerophylla is a sister species to C. fargesii in Fagaceae.

| S-EPMC7781992 | biostudies-literature

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships.

Project description:Fagus longipetiolata Seemen is a deciduous tree of the Fagus genus in Fagaceae, which is endemic to China. In this study, we successfully sequenced the cp genome of F. longipetiolata, compared the cp genomes of the Fagus genus, and reconstructed the phylogeny of Fagaceae. The results showed that the cp genome of F. longipetiolata was 158,350 bp, including a pair of inverted repeat (IRA and IRB) regions with a length of 25,894 bp each, a large single-copy (LSC) region of 87,671 bp, and a small single-copy (SSC) region of 18,891 bp. The genome encoded 131 unique genes, including 81 protein-coding genes, 37 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs), and 5 pseudogenes. In addition, 33 codons and 258 simple sequence repeats (SSRs) were identified. The cp genomes of Fagus were relatively conserved, especially the IR regions, which showed the best conservation, and no inversions or rearrangements were found. The five regions with the largest variations were the rps12, rpl32, ccsA, trnW-CCA, and rps3 genes, which spread over in LSC and SSC. The comparison of gene selection pressure indicated that purifying selection was the main selective pattern maintaining important biological functions in Fagus cp genomes. However, the ndhD, rpoA, and ndhF genes of F. longipetiolata were affected by positive selection. Phylogenetic analysis revealed that F. longipetiolata and F. engleriana formed a close relationship, which partially overlapped in their distribution in China. Our analysis of the cp genome of F. longipetiolata would provide important genetic information for further research into the classification, phylogeny and evolution of Fagus.

| S-EPMC8778281 | 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