Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Mangifera sylvatica Roxb. (Anacardiaceae) and its phylogenetic analysis.

ABSTRACT: In this study, we firstly reported the complete chloroplast (cp) genome sequences of the Mangifera sylvatica from Nanning, Guangxi province, China. The complete wild mango cp genome size is 158063 bp with a typical small single-copy region (SSC, 18340 bp), a large single-copy region (LSC, 87008 bp) and a pair of inverted repeats (IRs, 26379 bp and 26379 bp respectively). Out of 112 unique annotated genes in mango cp genome, 78 found to be protein coding, 30 to be tRNA and 4 rRNA genes. Besides, we found 51 microsatellite sequences (SSRs) in the cp genome. Sequence alignment and ML analysis of 29 full plastome data revealed M. sylvatica shares the closest relationship with cultivated mango (M. indica) and form a sister group with Rhus chinensis within Anacardiaceae.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC7748516 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance.

Project description:Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

| S-EPMC7011389 | biostudies-literature

The complete chloroplast genome sequence of Rhus chinensis Mill (Anacardiaceae).

Project description:In this study, complete chloroplast genome sequences of Rhus chinensis was characterized by de novo assembly using whole genome sequence data. The chloroplast genome of R. chinensis were 149,011bp long, which was comprised of a large single copy region of 96,882 bp, a small single copy region of 18,647bp, and a pair of inverted repeats of 16,741 bp. The genome contained 77 protein-coding genes, four rRNA genes and 30 tRNA genes. Phylogenetic tree revealed that R. chinensis was closely grouped with Spondias species, S. tuberosa and S. bahiensis, belonging to the Anacardiaceae family.

| S-EPMC7871870 | 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 Paeonia ostii.

Project description:Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the chloroplast genome of Paeonia ostii. We sequenced and analyzed the complete chloroplast genome of P. ostii. The size of the P. ostii chloroplast genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii chloroplast genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonialudlowii than to Paeoniaobovata and Paeoniaveitchii. The results of this study provide an assembly of the whole chloroplast genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.

| S-EPMC6017096 | 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

Complete chloroplast genome sequence and phylogenetic analysis of Erysimum cheiranthoides.

Project description:Erysimum cheiranthoides is commonly known as treacle-mustard or wormseed wallflower with value for reducing high temperature and inducing diuresis. Here, we characterized the complete chloroplast (cp) genome of E. cheiranthoides using genome skimming sequencing. The circular complete cp genome is 154,611?bp in length, containing a large single-copy (LSC) region of 83,809?bp, two copies of IR (26,475?bp each) regions, and a small single-copy (SSC) region of 17,852?bp. It comprises 113 unique genes, including 79 different protein-coding genes, 30 tRNA genes, and 4 rRNA genes with 19 duplicated genes in the IR regions. Phylogenetic analysis suggests that E. cheiranthoides is sister to Olimarabidopsis pumila with full support value in Brassicaceae.

| S-EPMC7706721 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Camellia fraterna.

Project description:Camellia fraterna belongs to the genus Camellia in the family Theaceae. We sequenced and analyzed the complete chloroplast genome of C. fraterna by Illumina sequencing in this study. The full length of the complete chloroplast genome is 156,902 bp, containing a pair of inverted repeat regions of 26,030 bp (IRa and IRb) separated by a large single-copy (LSC) region of 86,583 bp and a small single-copy (SSC) region of 18,259 bp. The C. fraterna chloroplast genome encodes 135 genes, comprising 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and three pseudogenes. This study will be useful for further study on genetic diversity and molecular breeding.

| S-EPMC7759240 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Torenia fournieri.

Project description:Torenia fournieri belongs to the genus Torenia in the family Linderniaceae. The complete chloroplast genome of T. fournieri was sequenced and analyzed by Illumina sequencing in this study. The full length of the complete chloroplast genome is 153,938 bp, containing a pair of inverted repeat regions of 24,805 bp (IRa and IRb) separated by a large single copy region (LSC) of 85,498 bp and a small single copy region (SSC) of 18,830 bp. The T. fournieri chloroplast genome encodes 131 genes, comprising 87 protein-coding genes, 36 tRNA genes, 8 rRNA genes, without pseudogene. Phylogenetic analysis showed that T. fournieri was closely related to T. benthamiana and T. concolor within the genus Torenia in family Linderniaceae.

| S-EPMC8204956 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Annona reticulata.

Project description:Annona reticulata is native to South and Central America which has many phytochemical and pharmacological activities suggesting a wide range of clinical application in lieu of cancer chemotherapy. This study provides abundant genomic data for the genetic relationship study, germplasm resources evaluation and varieties selection of A. reticulata. The complete chloroplast genome of A. reticulata was sequenced, assembled, and annotated in this study. The genome size was 201,906 bp and was divided into four regions: a large single-copy region of 69,650 bp, a small single-copy region of 3,014 bp, and two inverted repeat regions of 64,621 bp. A total number of 164 genes were annotated, including 115 protein-coding genes, one pseudogene, 40 tRNA genes, and eight rRNA genes. In terms of gene function, the 164 genes were divided into four major groups: genes for self-replication, photosynthesis, unknown function, and other genes. A maximum likelihood tree based on the chloroplast genome sequences of 24 plant species was constructed. The result of phylogenetic analysis showed that A. cherimola had the closest relationship with A. reticulate.

| S-EPMC7782357 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Syzygium malaccense.

Project description:Syzygium malaccense is native to Malaysia. It is sometimes called the malay apple, malay rose-apple, mountain rose-apple, mountain apple, water apple, or French cashew. The tree is very popular in many tropical and subtropical regions for its fruit and traditional medicine. The first complete chloroplast genome of Syzygium malaccense has been reported in this study. The complete chloroplast genome of Syzygium malaccense is 158,954 bp, composed of four regions: a large single-copy region with a size of 87,991 bp, a small single copy region with a size of 18,793 bp, and two inverted repeat regions with a size of 26,085 bp. The GC content is 36.97%. A total of 132 genes were annotated, including 84 encoding proteins, eight encoding rRNA genes, 37 encoding tRNA genes, and three encoding pseudo genes. Phylogenetic analysis showed that Syzygium aromaticum, Syzygium cumini, and Syzygium forrestii are closely related to Syzygium malaccense.

| S-EPMC7782888 | 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