Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The plastid genome of a narrowly distributed species Artocarpus petelotii (Moraceae).

ABSTRACT: The complete chloroplast genome sequence of Artocarpus petelotii was determined, a narrowly distributed species at high altitudes in the family Moraceae. To better determine its phylogenetic location with respect to the other Moraceae species, the complete plastid genome of A. petelotii was sequenced. The whole chloroplast genome is 161,009 bp in length, consisting of a pair of inverted repeat (IR) regions of 25,682 bp, one large single-copy (LSC) region of 89,552 bp, and one small single-copy (SSC) region of 20,093 bp. The overall GC content of the whole chloroplast genome is 35.8%. Further, maximum likelihood phylogenetic analysis was conducted using 26 complete plastomes of the Moraceae, which support close relationships among A. petelotii, A. nanchuanensis and A. heterophyllus.

SUBMITTER: Chen H

PROVIDER: S-EPMC7889096 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Artocarpus heterophyllus (Moraceae).

Project description:The Artocarpus heterophyllus, native to Western Ghats of India, Malaysia and south-eastern Asia, is a tree member of the mulberry family (Moraceae). Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of A. heterophyllus for the first time. The chloroplast genome is 160,387?bp long and includes 113 genes. Its LSC, SSC and IR regions are 88,422, 18,869 and 26,548?bp long, respectively. Phylogenetic tree analysis exhibited that A. heterophyllus was clustered with other Moraceae species with high bootstrap values.

| S-EPMC7800895 | biostudies-literature

The complete chloroplast genome of Artocarpus altilis (Moraceae) and phylogenetic relationships.

Project description:The chloroplast (cp) is an essential organelle in higher plants. The genes of the plastome are well suited to infer phylogenetic relationships among taxa. In this study, we report the assembly of the cp genome of Artocarpus altilis and its phylogeny among species from Moraceae family. The cp genome of A. altilis was 160,822 base pair (bp) in length, comprising one large single-copy region of 88,692 bp, one small single-copy region of 19,290 bp, and a pair of inverted repeat regions (IRs) of 26,420 bp. A total of 113 different genes were predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis of 19 species belonging to the Moraceae family confirmed the phylogenetic proximity of the genus Artocarpus and Morus and the genetic similarity of A. camansi and A. altilis.

| S-EPMC8284141 | biostudies-literature

Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species.

Project description:UNLABELLED: PREMISE OF THE STUDY:Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • METHODS AND RESULTS:A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • CONCLUSIONS:These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

| S-EPMC4103128 | biostudies-literature

The complete chloroplast genome of Epimedium pudingense (Berberidaceae), a narrowly distributed plant species in China.

Project description:Epimedium L. is the largest herbaceous genus of Berberidaceae which comprises more than 60 species. Epimedium pudingense is a rare plant species only narrowly inhabited in the Puding County in the Guizhou Province of China. Here, we first report the complete chloroplast genome of E. pudingense assembled from Illumina short-read sequencing data. The chloroplast genome of E. pudingense was 157,325 bp in length, with a total GC content of 36.11%. A total of 112 unique genes were identified, among which are 78 protein-coding genes, 30 tRNA genes and four rRNA genes. The phylogenetic analysis revealed that E. pudingense closely related to E. elachyphyllum. Our study will provide useful fundamental data for further phylogenetic and evolutionary studies of the Epimedium genus.

| S-EPMC7782884 | biostudies-literature

The complete chloroplast genome sequence of Artocarpus gomezianus (Moraceae) from Xishuangbanna, China.

Project description:Artocarpus gomezianus is a medicinal species native to Asia. To infer its phylogenetic relationship to the other Moraceae, the complete chloroplast genome of A. gomezianus was sequenced. The whole chloroplast genome is 160,743 bp in length, consisting of a pair of inverted repeat (IR) regions of 25,691 bp, one large single-copy (LSC) region of 89,241 bp, and one small singlecopy (SSC) region of 20,120 bp. The overall GC content of the complete chloroplast genome is 35.81%. Maximum likelihood analysis using 11 complete plastomes of the Moraceae and Cannabis sativa (Cannabaceae) designated as the outgroup, resolved A. gomezianus in a clade with A. petelotii and A. hypargyreus. These phylogenetic results are not consistent with previous findings based on nuclear loci in which A. gomezianus was grouped as a sister to a clade containing A. petelotii and A. hypargyreus. The complete chloroplast genome of A. gomezianus will provide a powerful tool to accelerate pharmacological development, systematics, and future phylogenetic studies in the Moraceae.

| S-EPMC8439205 | biostudies-literature

A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree.

Project description:Artocarpus nanchuanensis (Moraceae), which is naturally distributed in China, is a representative and extremely endangered tree species. In this study, we obtained a high-quality chromosome-scale genome assembly and annotation information for A. nanchuanensis using integrated approaches, including Illumina, Nanopore sequencing platform, and Hi-C. A total of 128.71 Gb of raw Nanopore reads were generated from 20-kb libraries, and 123.38 Gb of clean reads were obtained after filtration with 160.34× coverage depth and a 17.48-kb average read length. The final assembled A. nanchuanensis genome was 769.44 Mb with a 2.09 Mb contig N50, and 99.62% (766.50 Mb) of the assembled data was assigned to 28 pseudochromosomes. In total, 39,596 genes (95.10%, 39,596/41,636) were successfully annotated, and 129 metabolic pathways were detected. Plants disease resistance/insect resistance genes, plant-pathogen interaction metabolic pathways, and abundant biosynthesis pathways of vitamins, flavonoid, and gingerol were detected. Unigene reveals the basis of species-specific functions, and gene family in contraction and expansion generally implies strong functional differences in the evolution. Compared with other related species, a total of 512 unigenes, 309 gene families in contraction, and 559 gene families in expansion were detected in A. nanchuanensis. This A. nanchuanensis genome information provides an important resource to expand our understanding of the unique biological processes, nutritional and medicinal benefits, and evolutionary relationship of this species. The study of gene function and metabolic pathway in A. nanchuanensis may reveal the theoretical basis of a special trait in A. nanchuanensis and promote the study and utilization of its rare medicinal value.

| S-EPMC9197682 | biostudies-literature

The complete plastid genome of Ficus erecta (Moraceae).

Project description:Ficus erecta is a wild relative of F. carica, which is an important economic plant. Here, we determined the complete plastid genome of F. erecta using the Illumina paired reads to provide genomic feature resources. The whole plastid genome of F. erecta is 160,603 bp in length, containing two inverted repeats (IRs) of 25,899 bp separated by a large single-copy (LSC 88,640 bp) region and a small single-copy (SSC 20,165 bp) region. The complete plastome sequence of Ficus erecta will provide a useful resource for the evolutionary biology study as well as for the phylogenetic studies.

| S-EPMC7783041 | biostudies-literature

Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences.

Project description:PREMISE OF THE STUDY:Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. METHODS AND RESULTS:Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. CONCLUSIONS:These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit.

| S-EPMC4578378 | biostudies-literature

Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery.

Project description:PREMISE OF THE STUDY:We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae. METHODS AND RESULTS:A de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus. CONCLUSIONS:This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes.

| S-EPMC4948901 | biostudies-literature

Development and characterization of EST-SSR markers for Artocarpus hypargyreus (Moraceae).

Project description:PREMISE OF THE STUDY:Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. METHODS AND RESULTS:Based on the transcriptome data of A. hypargyreus, 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus. The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. CONCLUSIONS:These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus. Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus, indicating that they will be of great value for genetic study across this genus.

| S-EPMC5238703 | 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