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 of Lonicera similis Hemsl. and its phylogenetic analysis

ABSTRACT: Abstract Lonicera similis Hemsl. belongs to the Caprifoliaceae family and used as a substitute for ‘jin yin hua’. Recent years, it demonstrates great economic value because of its rich chemical composition. However, the phylogenetic relationship between L. similis and other family members remains unclear. In this paper, we assembled the cp genome of L. similis using the high-throughput Illumina pair-end sequencing data. The circular cp genome was 155,207 bp in size, including a large single-copy (LSC) region of 88994 bp and a small single-copy (SSC) region of 18,633 bp, which were separated by two inverted repeat (IR) regions (23,790 bp each). A total of 121 genes were predicted, including eight ribosomal RNAs (rRNAs), 36 transfer RNAs (tRNAs), and 77 protein-coding genes (PCGs). In addition, the result of phylogenetic analysis indicated that L. similis formed a close relationship from another congeneric species (Lonicera confusa). This study provides helpful information for future genetic study of L. similis.

SUBMITTER: Wu S

PROVIDER: S-EPMC8567915 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Lonicera similis (Caprifoliaceae).

Project description:The complete chloroplast genome of Lonicera similis Hemsl. has been characterized by reference-based assembly using Illumina paired-end data. The circular complete cp genome is 155,463 bp in length, containing a large single copy (LSC) region of 89,282 bp, a small single copy (SSC) region of 18,661 bp, which are separated by a pair of inverted repeat (IR) regions of 23,760 bp. A total of 129 genes were predicted from the cp genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis reveals that L. similis is more closely related to Lonicera japonica Thunb. and Lonicera dasystyla Rehd. Our result will provide a reference for the phylogenetic relationship, plant identification and resource development and utilization of Lonicera species.

| S-EPMC8480604 | biostudies-literature

The complete chloroplast genome of Litsea molis Hemsl. (Lauraceae): genome structure and phylogenetic analysis.

Project description:Litsea molis Hemsl. is a precious wild aromatic oil tree species and important medicinal plant. In this study, we sequenced and characterized the chloroplast genome of L. molis for the first time. Its complete chloroplast genome is 152,311 bp in length, containing a large single copy region of 93,258 bp and a small single copy region of 18,917 bp separated by a pair of inverted repeat regions of 20,068 bp. The chloroplast genome contains 130 unique genes, including 85 protein-coding genes, 37 tRNA and 8 rRNA genes. Phylogenetic analysis based on chloroplast genome sequences of 36 plants from the family Lauraceae showed that L. molis is more closely related to species of Lindera genus than other genera in Lauraceae.

| S-EPMC7832512 | biostudies-literature

The complete chloroplast genome of Lonicera pampaninii Levl. and its phylogenetic analysis.

Project description:Lonicera pampaninii Levl, a Chinese herbal medicine widely used in the folk, has the effect of clearing away heat and detoxifying similar to other plants of the Lonicera. However, its genetic relationship with these plants is unclear. In this work, the cp genome of Lonicera pampaninii Levl. was assembled by the high-throughput Illumina pair-end sequencing data. The circular cp genome is 155,249 bp in size, including a large single-copy (LSC) region of 89,068 bp and a small single-copy (SSC) region of 18,635 bp, which were separated by two inverted repeat (IR) regions (23,773 bp each). A total of 120 genes were predicted, including eight ribosomal RNAs (rRNAs), 33 transfer RNAs (tRNAs), and 79 protein-coding genes (PCGs). Furthermore, phylogenetic analysis revealed a strong sister relationship between L. pampaninii and other two congeneric species (Lonicera confusa and Lonicera japonica). This study provides useful information for future genetic study of L. pampaninii.

| S-EPMC8462834 | biostudies-literature

The complete chloroplast genome of Lonicera fulvotomentosa Hsu et S. C. Cheng and its phylogenetic analysis.

Project description:Lonicera fulvotomentosa Hsu et S. C. Cheng is widely used as an edible and medicinal food in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. fulvotomentosa and other family members remains unclear. In this work, we assembled the cp genome of L. fulvotomentosa using the high-throughput Illumina pair-end sequencing data. The circular cp genome is 155,102 bp in size, including a large single-copy (LSC) region of 88,906 bp and a small single-copy (SSC) region of 18,628 bp, which were separated by two inverted repeat (IR) regions (23,784 bp each). A total of 129 genes were predicted, including eight ribosomal RNAs (rRNAs), 39 transfer RNAs (tRNAs), and 82 protein-coding genes (PCGs). Furthermore, phylogenetic analysis revealed that L. fulvotomentosa formed a different clade from other two congeneric species (Lonicera confuse and Lonicera japonica). This study provides useful information for future genetic study of L. fulvotomentosa.

| S-EPMC7971229 | biostudies-literature

The complete chloroplast genome of Castanopsis carlesii (Hemsl.) Hay.

Project description:Castanopsis carlesii (Hemsl.) Hay. is a widely distributed and dominant tree species with significant ecological and economical values. In this study, the complete chloroplast genome sequence of C. carlesii was reported using the Illumina Hiseq 2500 platform. The complete chloroplast genome was 160,205?bp forming a typical quadripartite structure, with a pair of inverted repeated (IRs) regions of 25,670?bp, a large single copy (LSC) region of 89,849?bp, and a small single copy (SSC) region of 19,016?bp. A total of 124 functional genes were annotated, including 79 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The ML phylogenetic analysis showed that the genus Castanopsis formed a clade except Castanopsis fargesii.

| S-EPMC7706500 | biostudies-literature

The complete chloroplast genome of Styrax confusus Hemsl. (Styracaceae).

Project description:Styrax confusus Hemsl. is valued for its beauty and fragrance. Here, we characterized the complete chloroplast (cp) genome of S. confusus using next-generation sequencing. The circular complete cp genome of S. confusus was 157,981 bp in length, containing a large single-copy (LSC) region of 87,571 bp, and a small single-copy (SSC) region of 18,316 bp. It comprises 133 genes, including eight rRNA genes, 37 tRNA genes, and 88 protein-coding genes. The GC content of S. confusus cp genome is 36.95%. A phylogenetic tree reconstructed by 30 chloroplast genomes reveals that S. confusus is mostly related to Styrax calvescens Perk.

| S-EPMC7748495 | biostudies-literature

Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.

Project description:The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L. japonica cp genome had a unique rearrangement between trnI-CAU and trnN-GUU. In L. japonica cpDNA, rps19, rpl2, and rpl23 move to the LSC region, from the IR region. The ycf1 pesudogene in the IR region is lost, and only one copy locates in the SSC region. Comparative cp DNA sequence analyses of L. japonica with other cp genomes reveal that the gene order, and the gene and intron contents, are slightly different. The introns in ycf2 and rps18 genes are found for the first time. Four genes (clpP, petB, petD, and rpl16) lost introns. However, its genome structure, GC content, and codon usage were similar to those of typical angiosperm cp genomes. All preferred synonymous codons were found to use codons ending with A/T. The AT-rich sequences were less abundant in the coding regions than in the non-coding ones. A phylogenetic analysis based on 71 protein-coding genes supported the idea that L. japonica is a sister of the Araliaceae species. This study identified unique characteristics of the L. japonica cp genome that contribute to our understanding of the cpDNA evolution. It offers valuable information for the phylogenetic and specific barcoding of this medicinal plant.

| S-EPMC6155926 | biostudies-literature

Characterization of the complete chloroplast genome of Lonicera macranthoides.

Project description:Lonicera macranthoides is an important Chinese traditional medicine plant which is endemic in southwest China. The complete chloroplast genome from L. macranthoides is determined in this study. The genome size was 154,897 bp, containing a large single copy (LSC) region of 88,692 bp and a small single copy (SSC) region of 18,623 bp, which were separated by a pair of 23,786 bp inverted repeat (IR) regions. The plastome contained 130 genes, including 81 protein-coding genes (77 PCG species), eight ribosomal RNA genes (4 rRNA species), 39 tRNA genes (29 tRNA species) and two pseudognes. The most of gene species occurred as a single copy, while 13 gene species occurred in double copies, including all rRNA species, six tRNA species and three PCG species, and two tRNA genes occur in treble copies. Finally, phylogenetic analysis demonstrated that L. macranthoides is closely related to L. japonica, and genus Lonicera shows a closer relationship with Triostrum for the current data.

| S-EPMC7799602 | biostudies-literature

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus.

Project description:We sequenced and analyzed the complete chloroplast genome of Aster tataricus (family Asteraceae), a Chinese herb used medicinally to relieve coughs and reduce sputum. The A. tataricus chloroplast genome was 152,992 bp in size, and harbored a pair of inverted repeat regions (IRa and IRb, each 24,850 bp) divided into a large single-copy (LSC, 84,698 bp) and a small single-copy (SSC, 18,250 bp) region. Our annotation revealed that the A. tataricus chloroplast genome contained 115 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. In addition, 70 simple sequence repeats (SSRs) were detected in the A. tataricus chloroplast genome, including mononucleotides (36), dinucleotides (1), trinucleotides (23), tetranucleotides (1), pentanucleotides (8), and hexanucleotides (1). Comparative chloroplast genome analysis of three Aster species indicated that a higher similarity was preserved in the IR regions than in the LSC and SSC regions, and that the differences in the degree of preservation were slighter between A. tataricus and A. altaicus than between A. tataricus and A. spathulifolius. Phylogenetic analysis revealed that A. tataricus was more closely related to A. altaicus than to A. spathulifolius. Our findings offer valuable information for future research on Aster species identification and selective breeding.

| S-EPMC6222381 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'.

Project description:Spathiphyllum is a very important tropical plant used as a small, potted, ornamental plant in South China, with an annual output value of hundreds of millions of yuan. In this study, we sequenced and analyzed the complete nucleotide sequence of the Spathiphyllum 'Parrish' chloroplast genome. The whole chloroplast genome is 168,493 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 31,600 bp), separated by a small single-copy (SSC, 15,799 bp) region and a large single-copy (LSC, 89,494 bp) region. Our annotation revealed that the S. 'Parrish' chloroplast genome contained 132 genes, including 87 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In the repeat structure analysis, we detected 281 simple sequence repeats (SSRs) which included mononucleotides (223), dinucleotides (28), trinucleotides (12), tetranucleotides (11), pentanucleotides (6), and hexanucleotides (1), in the S. 'Parrish' chloroplast genome. In addition, we identified 50 long repeats, comprising 18 forward repeats, 13 reverse repeats, 17 palindromic repeats, and 2 complementary repeats. Single nucleotide polymorphism (SNP) and insertion/deletion (indel) analyses of the chloroplast genome of the S. 'Parrish' relative S. cannifolium revealed 962 SNPs in S. 'Parrish'. There were 158 indels (90 insertions and 68 deletions) in the S. 'Parrish' chloroplast genome relative to the S. cannifolium chloroplast genome. Phylogenetic analysis of five species found S. 'Parrish' to be more closely related to S. kochii than to S. cannifolium. This study identified the characteristics of the S. 'Parrish' chloroplast genome, which will facilitate species identification and phylogenetic analysis within the genus Spathiphyllum.

| S-EPMC6808432 | 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