Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete plastome sequence of Illigera grandiflora.

ABSTRACT: Illigera grandiflora, a kind of traditional medicinal liana, belongs to the Illigera Blume of the Hernandiaceae. In this study, we reported the characteristics of complete plastome for I. grandiflora. Its total plastome was 156,138 bp in length, comprising a large single-copy region(LSC) of 84,931 bp, a small single-copy region (SSC) of 18,544 bp, and a pair of inverted repeat (IR) regions of 26,549 bp. The overall GC content was 39.16% (LSC, 37.77%; SSC, 33.89%; IR, 43.21%). The plastome encoded 134 genes, including 83 protein-coding genes, 42 transfer RNA genes, and 10 ribosomal RNA genes. The relationships in our phylogeny showed that the two Illigera species are located in the same clade, with Hernandia nymphaeifolia being the next sister group, followed by Wilkiea huegeliana.

SUBMITTER: Qu Y

PROVIDER: S-EPMC8284138 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete plastome sequence of Lilium Bulbiferum (Liliaceae).

Project description:The flower shape of Lilium bulbiferum L. is different from that of the other European lilies. The phylogenetic position of the plant has been changed frequently. In the present study, we have sequenced the complete plastome of L. bulbiferum. The plastome sequence was 152,686?bp long, with a large single copy (LSC) region of 82,083?bp, a small single copy (SSC) region of 17,619?bp, and two inverted repeat (IR) regions of 26,492?bp each. It contained 133 genes, including 83 coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 4 pseudogenes. The GC contents of LSC, SSC, and IT were 34.8%, 30.7%, and 42.5%, respectively, corresponding to 37.0% of the total GC content. The phylogenetic position of L. bulbiferum was closely related to the north-eastern lilies.

| S-EPMC7800588 | biostudies-literature

The complete plastome sequence of Momordica cochinchinensis (Cucurbitaceae).

Project description:Momordica cochinchinensis (Lour.) Spreng. is an important medicinal plant that is used to treat various diseases in South and Southeast Asia. In this study, the complete plastome of M. cochinchinensis was sequenced and found to exhibit a total length of 158,955 bp, with a large single copy (LSC) region of 87,924 bp and a small single copy (SSC) region of 18,479 bp, as well as with two inverted repeats (IRs) that were both 26,726 bp in length. In total, 129 genes were detected, comprising 86 protein-encoding genes, 8 ribosomal RNA (rRNA) genes, and 35 transfer RNA (tRNA) genes. Furthermore, the inferred phylogenetic tree confirmed that M. cochinchinensis belongs to the genus Momordica in the Cucurbitaceae family. The research results will be used for authenticating M. cochinchinensis plant materials and for analyzing the genetic diversity and phylogenetic relationships in Momordica.

| S-EPMC9980024 | biostudies-literature

Complete plastome sequence of Averrhoa carambola L. (Oxalidaceae).

Project description:In this study, we determined the complete plastome sequence of Averrhoa carambola L. (Oxalidaceae) (NCBI acc. no. KX364202). To the best of our knowledge, this is the first reported complete plastome sequence from the order Oxalidales. The gene order and structure of the A. carambola plastome are collinear with the typical plastome of land plants. The complete plastome size is 155,965 bp in length and consists of a large single copy region of 87,217 bp and a small single copy region of 17,496 bp, which are separated by a pair of 25,626-bp-long inverted repeat regions. The overall A-T content of the plastome sequence is 61.2%. The plastome contains 111 genes, of which 77 are protein-coding genes, 30 are tRNA genes, and 4 are rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 91 simple sequence loci were identified from the genome. Phylogenetic analysis revealed that A. carambola is a sister group of Euonymus japonicus with 100% bootstrap support.

| S-EPMC7799573 | biostudies-literature

Complete plastome sequence of Psidium guajava L. (Myrtaceae).

Project description:In this study, we determined the complete plastome sequence of Psidium guajava L. (Myrtaceae) (NCBI acc. no. KX364403). The gene order and structure of the P. guajava plastome are similar to those of a typical angiosperm. The complete plastome is 158,841 bp in length, and consists of a large single copy of 87,675 bp and a small single copy of 18,464 bp, separated by two inverted repeats of 26,351 bp. The overall AT content of the sequence is 63.0%. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 100 simple sequence loci were identified from the genome. Phylogenetic analysis revealed that P. guajava is a sister group of Eugenia uniflora with 100% bootstrap support.

| S-EPMC7800272 | biostudies-literature

Complete plastome sequence of Xylosma longifolia Clos. (Salicaceae).

Project description:Xylosma longifolia is a tree species within Salicaceae and is distributed in Guizhou, Yunnan, Fujian, Guangxi, Guangdong, and Hainan provinces of China as well as in Vietnam, Laos, and India. There are no studies utilizing the complete plastome of Xylosma longifolia in the current literature. Therefore, this report provides a reference for the plastid gene sequence of Xylosma longifolia, and it contributes to the phylogenetic placement and species identification. In this report, we described the complete plastome sequence of Xylosma longifolia. The complete plastome length of Xylosma longifolia is 156,938 bp and has the typical quadripartite structure and gene content of angiosperms, including two inverted repeat (IR) regions of 27,514 bp, a large single-copy (LSC) region of 85,221 bp and a small single-copy (SSC) region of 16,689 bp. The plastome contains 130 genes, including 86 protein coding genes, 36 tRNA genes, eight rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA). The GC content of the plastome is 36.8%. The complete plastome sequence will be a valuable resource for studies involving the phylogenetic inference of Salicaceae.

| S-EPMC7995910 | biostudies-literature

Complete plastome sequence of Phalaenopsis cornu-cervi (Vandeae, Orchidaceae).

Project description:Phalaenopsis cornu-cervi is a taxonomically and horticulturally important moth orchid. In this study, we report and characterize the complete plastid genome sequence of P. cornu-cervi for the first genomic resources in section Polychilos. Its complete plastome is 147,241?bp in length and contains two inverted repeat (IR) regions of 25,005bp, a large single-copy (LSC) region of 85,714?bp, and a small single-copy (SSC) region of 11,517?bp. The plastome contains 110 genes, consisting of 76 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. It also shows the typical characteristics of Phalaenopsis chloroplast genome, while all ndh genes are non-functional. The complete plastome sequence of P. cornu-cervi will provide a useful resource for future phylogenetic study of Phalaenopsis and its garden utilization.

| S-EPMC7707187 | biostudies-literature

Complete plastome sequence of Rhodoleia championii Hook. f. (Hamamelidaceae).

Project description:The complete chloroplast genome of Rhodoleia championii (Hamamelidaceae) was firstly reported in this study. The complete chloroplast genome of R. championii is 159,115?bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 88,123?bp), a single-copy region (SSC, 18,131?bp) and a pair of inverted repeats (IRs, 26,420?bp). There are 114 genes annotated, including 80 unique protein-coding genes, 4 unique ribosomal RNA genes, and 30 transfer RNA genes. According to the phylogenetic tree of R. championii and the other 9 species, R. championii was closely related to Chunia bucklandioides.

| S-EPMC7707384 | biostudies-literature

Complete plastome sequence of Manilkara zapota (L.) P.Royen (Sapotaceae).

Project description:iThe plastome of Manilkara zapota is found to be 158,386?bp long with the typical quadripartite structure of angiosperms, contains two inverted repeats (IRs) of 26,099?bp each, a large single-copy (LSC) region of 87,745?bp, and a small single-copy (SSC) region of 18,443?bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of M. zapota is 63.00%. The phylogenetic analysis indicated that M. zapota is close to Sideroxylon wightianum within Sapotaceae in this study.

| S-EPMC7706626 | biostudies-literature

The complete plastome sequence of Lilium wahingtonianum Kellogg (Liliaceae).

Project description:Lilium washingtonianum Kellogg is native to Western America and grows on slope in high subalpine. In the present study, the complete plastome of L. washingtonianum was sequenced. The plastome sequence was 151,967?bp long, with a large single copy region of 81,393?bp, a small single copy region of 17,352?bp, and two inverted repeat regions of 26,611?bp each. Total 133 genes were identified, including 83 coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 4 pseudogenes. Among four pseudogenes, pseudo ndhF gene was the first to report among Lilium species so far. The phylogenetic position of L. washingtonianum was sister to L. superbum but American lilies were not monophyletic.

| S-EPMC7800384 | biostudies-literature

The complete plastome sequence of Pinellia peltata Pei (Araceae).

Project description:The complete plastome of Pinellia peltata is reported in this study. The whole plstome contains 164,293 bp, including a large single copy region (90,089 bp) and a small single copy region (24,871 bp), which were separated by a pair of inverted repeat regions (24,881 bp of IRB and 24,982 bp of IRA). Totally, 130 genes were identified, containing 86 coding-protein, 8 rRNA (4 rRNA species), and 36 tRNA genes. Phylogenetic analysis based on common protein coding genes of 10 Araceae species showed that P. peltata is original than other species in the genus Pinellia. The whole plastome of P. peltata and other species should facilitate further works for the genus Pinellia about genetic diversity, phylogenetic analysis, and so on.

| S-EPMC8245090 | 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