Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae.

ABSTRACT: Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.

SUBMITTER: Gu L

PROVIDER: S-EPMC8789150 | 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

Characterization of the complete chloroplast genome of Lonicera tatarica L. (Caprifoliaceae).

Project description:Lonicera tatarica L. is an excellent landscaping shrub with high ornamental value. Here, we report the complete chloroplast genome sequence of L. tatarica. The size of the chloroplast genome is 154,675 bp in length, including a large single copy region (LSC) of 88,361 bp, a small single copy region (SSC) of 18,750 bp, and a pair of inverted repeated regions of 23,782 bp. The L. tatarica chloroplast genome encodes 131 genes, including 85 protein-coding, 38 tRNA, and 8 rRNA genes. Phylogenetic analysis fully resolved L. tatarica in a clade with L. japonica, L. confusa, and L. maximowiczii. These data provide a useful resource when studying the genetic diversity of L. tatarica.

| S-EPMC8344791 | biostudies-literature

Characterization of the complete chloroplast genome of Lonicera japonica (Caprifoliaceae), a long history herb species plant from China.

Project description:Lonicera japonica is a common ornamental and medicinal plant in North America and East Asia. In this study, the complete chloroplast genome of L. japonica was presented and annotated. The chloroplast genome of L. japonica is 155,078?bp in length, which has a large single-copy (LSC) region of 88,859?bp, a small single-copy region (SSC) of 18,647?bp, and a pair of inverted-repeat (IRs) regions of 23,786?bp in each one. The overall nucleotide composition is 30.2% of A, 31.2% of T, 19.6% C, and 19.0% G, with a total A?+?T content of the chloroplast genome 61.4% and G?+?C content of 38.6%. The chloroplast genome of L. japonica contains 130 genes, including 83 protein-coding genes (PCGs), 39 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). Phylogenetic relationship used the maximum-likelihood (ML) method that L. japonica is closely related to Lonicera macranthoides. This study can use for medicinal valuable and clinical drug development for the future.

| S-EPMC7707689 | biostudies-literature

The complete chloroplast genome of the Lonicera maackii (Caprifoliaceae), an ornamental plant.

Project description:Lonicera maackii, is scattered in west and northeast China as well as adjacent Korea, Japan and the Soviet union. Here, we assembled and characterized the complete chloroplast (cp) genome of L. maackii using Illumina sequencing data for the first time. The complete cp genome was 155,337 bp in length, consisting of a pair of inverted repeats of 23,718 bp, a large single-copy region of 89,221 bp and a small single-copy region of 18,680 bp. The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on 25 complete cp genome sequences indicated that L. maackii is closely related to Lonicera sachalinensis and Lonicera insularis.

| S-EPMC7748521 | biostudies-literature

Complete chloroplast genome of Lonicera ligustrina Wall. (Caprifoliaceae) and its phylogenetic implications.

Project description:Lonicera ligustrina is a folk medicinal herb in China and India with highly potential medicinal value. Here, we reported the complete chloroplast (cp) genome of L. ligustrina (GenBank accession number: ON968694). The cp genome was 155,330 bp long, with a large single-copy region (LSC) of 88,855 bp and a small single-copy region (SSC) of 18,647 bp separated by a pair of inverted repeats (IRs) of 23,914 bp. We also reconstructed the phylogeny of Lonicera using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The current study indicated that L. ligustrina is sister with the Nintooa clade of subgen. Lonicera.

| S-EPMC10461517 | biostudies-literature

Characterization of the complete chloroplast genome of Lonicera tangutica (Caprifoliaceae), an ornamental and medicinal plant in China.

Project description:In the present study, the complete chloroplast genome of Lonicera tangutica is presented and characterized for the first time. The complete chloroplast genome was 156,121 bp in length, including 23,899 bp inverted repeat (IR) regions, an 89,466 bp large single-copy (LSC) region, and an 18,851 bp small single-copy (SSC) region. A total of 129 genes, including 37 tRNA genes, eight rRNA genes, and 84 protein-coding genes, were annotated, and the overall GC content of the chloroplast genome was 38.35%. Two introns in the ycf3 gene and a single intron in another gene were detected. Maximum-likelihood phylogenetic analysis indicated that L. tangutica has a very close evolutionary relationship with Lonicera praeflorens, Lonicera hispida, Lonicera fragrantissima, and Lonicera stephanocarpa. These results are valuable for studying the evolution and genetic diversity of L. tangutica.

| S-EPMC8959524 | biostudies-literature

The complete chloroplast genome of Lonicera hypoglauca Miq (Caprifoliaceae: Dipsacales) from Guangxi, China.

Project description:Lonicera hypoglauca Miq, which is widely distribute in south China, is an important Chinese plant used in traditional medicine. Here we report the first complete chloroplast (cp) genome sequence of this species. The circular cp genome is 154,581 bp in size, including a large single-copy (LSC) region of 88,379 bp and a small single-copy (SSC) region of 18,646 bp, which were separated by two inverted repeat (IR) regions (IRA and B, 23,778 bp each). A total of 121 genes were annotated, including 8 ribosomal RNAs (rRNAs), 33 transfer RNAs (tRNAs) and 80 protein-coding genes (PCGs). Phylogenetic analysis of 20 representative members within the Caprifoliaceae showed that L. hypoglauca is closely related to the Lonicera macranthoides. This study provides important genetic information for future systematic and evolutionary studies of L. hypoglauca.

| S-EPMC7872560 | biostudies-literature

Complete chloroplast genome and phylogenetic analysis of Lonicera caerulea var. edulis (Caprifoliaceae).

Project description:Lonicera caerulea var. edulis, known as "blue honeysuckle" or "Haskap," is a deciduous shrub that belongs to the Caprifoliaceae family. Characterized by the high cold hardiness and high quality of fruit, it has become a novel cash crop in cold regions worldwide. The lack of available chloroplast (cp) genome information limits studies of its molecular breeding and phylogeny. Here, the complete cp genome of Lonicera caerulea var. edulis was assembled and characterized for the first time. It was 155,142 bp in length with 38.43% of GC content, including 23,841 bp inverted repeat regions (IRs), an 88,737 bp large single-copy region (LSC), and an 18,723 bp small single-copy region (SSC). A total of 132 genes, including 85 protein-coding genes, 8 rRNA genes, and 39 tRNA genes were annotated. Phylogenetic analysis indicated that L. caerulea var. edulis was closely related to L. tangutica. These data and results provide a valuable resource for the development of breeding tools and genetic diversity studies for L. caerulea.

| S-EPMC9970238 | 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

Isolation and characterization of microsatellite loci from Amur honeysuckle, Lonicera maackii (Caprifoliaceae).

Project description:Lonicera maackii (Caprifoliaceae) is one of the most problematic invasive shrubs in forests of the eastern United States. Microsatellite markers could serve to test putative source-sink relationships among populations to determine whether invasions progress along expanding fronts or through long-distance dispersal events followed by local expansion. • Eleven microsatellite loci were developed for Amur honeysuckle using a modified magnetic bead protocol. Six loci were screened across 158 individuals from seven populations and were shown to be variable, with the number of alleles per locus ranging from seven to 16. Observed heterozygosity ranged from 0.655 to 0.757. Five additional loci were screened using 68 individuals from three different populations, with seven to 12 alleles per locus and observed heterozygosity ranging from 0.682 and 0.831. • These microsatellite markers will help to elucidate the genetic structure and patterns of dispersal of L. maackii in its invasive range.

| S-EPMC4103602 | 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