Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequences of Trapa acornis Nakano (Lythraceae).

ABSTRACT: Trapa L. (Lythraceae), also called water chestnut, is a genus widely distributed in the Old World. With the high edible and medical values, the water chestnut has been cultivated popularly in China since the Tang and Song Dynasties. Among all cultivars, T. acornis Nakano is one of the most current commercial one, which grown in Jiaxing, Zhejiang province, China. However, due to the limited availability of molecular marker resources of T. acornis, we still have difficulty in its identification and utilization. Here, we reported the complete chloroplast genome sequence of T. acornis. The result demonstrated that the chloroplast genome was 155,538 bp in length, consisting of a small single copy (SSC) region of 18,275 bp, a large single copy (LSC) region of 88,492 bp, and two inverted repeat (IR) regions of 24,386 bp. The chloroplast genome contains a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenomic analysis demonstrated the sister relationship between T. acornis and T. bicornis.

SUBMITTER: Yuan Y

PROVIDER: S-EPMC8667907 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Chloroplast genome of Trapa bispinosa Roxb. (Trapa, Lythraceae).

Project description:Trapa bispinosa Roxb. is an annual aquatic herb with great significance of medicinal, edible and economic value. Here, we reported the complete chloroplast genome sequence of Trapa bispinosa and conducted preliminary investigation of its phylogenetic relationship with other related species. As the result showed, the whole chloroplast genome size was 155,556 bp consisting of four adjoining regions, i.e., a large/small single copy (LSC, 88,506 bp/SSC, 18,274 bp) region and two inverted repeat (IRs, 24,388 bp) regions. Among 112 identified unique genes were 78 protein coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Trapa spp. were precisely clustered as a monophyly, and simultaneously, the closest relation between Trapa bispinosa and Trapa natans were strongly supported in the maximum likelihood analysis.

| S-EPMC7872573 | biostudies-literature

The complete chloroplast genome sequence of Trapa bicornis Osbeck (Lythraceae).

Project description:Trapa (Lythraceae) is an aquatic plant genus widely distributed in the old world. Although Trapa species have great edible and medical value, studies related to species identification and utilization are still lacking. Here, we reported the complete chloroplast genome sequence of a cultivated species, T. bicornis. The chloroplast genome size of T. bicornis was 155,539 bp, consisting of a pair of inverted repeat (IR) regions (24,386 bp), separated by a large single copy (LSC) region (88,493 bp) and a small single copy (SSC) region (18,274 bp). A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenomic analysis supported the monophyly of Trapa, and a sister relationship between T. bicornis and T. natans.

| S-EPMC7782891 | biostudies-literature

The complete chloroplast genome sequence of Trapa kozhevnikoviorum Pshenn. (Lythraceae).

Project description:Trapa (Lythraceae) is an economically important aquatic genus used for food and medicine, with wide distribution in Asia, Africa, and Europe. Identification of species, genetic studies and utilization of Trapa are limited by lack of molecular data. Herein, we report the complete chloroplast (cp) genome sequence of a wild species, Trapa kozhevnikoviorum Pshenn. The cp genome size of T. kozhevnikoviorum is 155,545 bp, consisting of a pair of inverted repeat regions (IRa/IRb) of length 24,388 bp, separated by the small single copy (SSC) region of 18,275 bp and a large single copy (LSC) region of 88,494 bp. A total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA were annotated. Phylogenetic analysis based on 15 whole cp genomes of Lythraceae species supported the monophyletic clustering of Trapa. A cladal relationship among T. kozhevnikoviorum, T. bicornis, and T. natans was revealed.

| S-EPMC8143615 | biostudies-literature

The complete chloroplast genome sequence of Trapa incisa Sieb. & Zucc. (Lythraceae).

Project description:Trapa L., an annual floating-leaved herb, is widely distributed in the old world and has important edible and medicinal values. However, the taxonomy and phylogeny of Trapa are unclear. Here, we reported the complete chloroplast genome of a wild species with small nuts, T. incisa. The complete chloroplast genome size of T. incisa was 155, 453 bp, consisting of two inverted repeat (IR) regions (24, 388 bp), one large single copy (LSC) region (88, 398 bp) and one small single copy (SSC) region (18, 279 bp). A total of 129 genes were annotated, including 83 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Among them, 19 genes were duplicated (6 protein-coding genes, 9 tRNA genes and 4 rRNA genes). The phylogenomic analysis suggested a close relationship between T. incisa and T. maximowiczii.

| S-EPMC8174476 | biostudies-literature

Complete chloroplast genome sequence of Punica granatum 'Nana' (Lythraceae) and phylogenetic analysis.

Project description:Pomegranate (Punica granatum L.) is of great significance both as a fruit tree and an ornamental plant. Hereon, we sequenced and characterized the complete chloroplast genome of Punica granatum 'Nana' and performed phylogenetic analysis concerning related species. It turned out that the length of chloroplast genome sequence reached 158,639 bp and exhibited a four-conjoined structure, i.e., a large single copy region (LSC, 89,022 bp), a small single copy region (SSC, 18,685 bp) and twain inverted repeat regions (IRa and IRb, 25,466 bp). 112 unique genes were identified, consisting of 78 protein-coding genes, four ribosomal RNA (rRNA) genes and 30 transfer RNA (tRNA) genes. The result of phylogenetic analysis based on Neighbor-joining (NJ) method was consistent with that of Bayesian inference (BI), which strongly supported that Punica granatum 'Nana' was close to its original species Punica granatum and they together had a close relationship with Heimia myrtifolia within Lythraceae.

| S-EPMC7510682 | biostudies-literature

The Complete Chloroplast Genome Sequences of Six Rehmannia Species.

Project description:Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order. The complete genomes ranged from 153,622 bp to 154,055 bp in length, including 133 genes encoding 88 proteins, 37 tRNAs, and 8 rRNAs. Three genes (rpoA, rpoC2, accD) have potentially experienced positive selection. Plastome size variation of Rehmannia was mainly ascribed to the expansion and contraction of the border regions between the inverted repeat (IR) region and the single-copy (SC) regions. Despite of the conserved structure in Rehmannia plastomes, sequence variations provide useful phylogenetic information. Phylogenetic trees of 23 Lamiales species reconstructed with the complete plastomes suggested that Rehmannia was monophyletic and sister to the clade of Lindenbergia and the parasitic taxa in Orobanchaceae. The interspecific relationships within Rehmannia were completely different with the previous studies. In future, population phylogenomic works based on plastomes are urgently needed to clarify the evolutionary history of Rehmannia.

| S-EPMC5368707 | biostudies-literature

The complete chloroplast genome of Lagerstroemia loudonii Teijsm. & Binn. (Lythraceae), an ornamental tree with medicinal value.

Project description:Lagerstroemia loudonii is an ornamental tree with medicinal value. Here, we announce the first complete chloroplast genome sequence of L. loudonii. The L. loudonii chloroplast genome harbors a typical quadripartite structure with a total length of 152,372 bp, including a large single-copy (LSC) region of 84,086 bp, a small single-copy (SSC) region of 16,798 bp, and two separated inverted repeat (IR) regions of 25,744 bp each. The chloroplast genome encodes 130 genes, including 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The GC content of the whole chloroplast genome is 37.6%. Phylogenetic analysis based on complete chloroplast genomes of L. loudonii and 17 other plant species revealed that Lagerstroemia is a separate genus, and L. loudonii is closely related to L. calyculata.

| S-EPMC9262357 | biostudies-literature

Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species.

Project description:BACKGROUND:Phoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus. RESULTS:We sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies. CONCLUSION:This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

| S-EPMC5597560 | biostudies-literature

Complete chloroplast genome sequences of Poikilospermum lanceolatum (Urticeae).

Project description:The complete chloroplast genome of Poikilospermum lanceolatum was sequenced using HiSeq4000 of Illumina. The length of this genome was 153, 454?bp, including a large single copy (LSC) region (84,202?bp), a small single copy (SSC) region (18,172?bp), and two inverted repeat (IR) regions (25,540?bp). The overall GC content of the genome of P. lanceolatum was 36.9%. The genome included 111 unique genes (78 protein-coding genes, 29 tRNA genes, and four rRNA genes). Phylogenetic analysis based on 67 protein-coding genes showed that Boehmerieae was sister to P. lanceolatum, with 100% bootstrap values.

| S-EPMC7687602 | biostudies-literature

The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae).

Project description:The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes. This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.

| S-EPMC5033369 | 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