Browse
Submit Data
Databases
API
Help

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete plastid genome of Lysimachia christinae Hance (Primulaceae).

ABSTRACT: Lysimachia christinae Hance is widely distributed in subtropical China at the elevational range from 500-2300 m. The species is an important medicinal herb for treating jaundice, urinary disorders, and the liver. Here, we sequenced and characterized the whole plastid genome of L. christinae. It is 154,810 bp in length, containing two copies of inverted repeat (IR) regions (26,034 bp, each), a large single-copy (LSC) region (84,809 bp), and a small single-copy (SSC) region (17,933 bp). It has 114 genes, of which 80 are protein-coding, 30 are tRNA, and 4 are rRNA genes. The ML tree indicates L. christinae is closely related to Lysimachia congestiflora Hemsl. This genome information can help us better construct a backbone phylogeny of Lysimachia in the future.

SUBMITTER: Zhang CY

PROVIDER: S-EPMC7850378 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete plastid genome of Lysimachia christinae Hance (Primulaceae).

Zhang Cai-Yun CY Yan Hai-Fei HF Wang Feng-Ying FY

Mitochondrial DNA. Part B, Resources 20210127 1

Lysimachia christinae Hance is widely distributed in subtropical China at the elevational range from 500-2300 m. The species is an important medicinal herb for treating jaundice, urinary disorders, and the liver. Here, we sequenced and characterized the whole plastid genome of L. christinae. It is 154,810 bp in length, containing two copies of inverted repeat (IR) regions (26,034 bp, each), a large single-copy (LSC) region (84,809 bp), and a small single-copy (SSC) region (17,933 b ...[more]

PMID: 33553641

Similar Datasets

Characterization of the plastid genome of the monotypic genus Bryocarpum (Primulaceae).

Project description:Bryocarpum Hook. f. & Thoms., a monotypic genus of Primulaceae, is narrowly distributed in the eastern Himalayas. In this study, the complete plastid genome of Bryocarpum himalaicum was characterized by Illumina paired-end sequencing reads. The plastid genome of B. himalaicum is 153,398 bp in length, including large single copy (LSC) region of 84,446 bp, small single copy (SSC) region of 17,564 bp, and two separated inverted regions (IRs) of 25,694 bp, each. It encodes 110 genes, of which 79 are protein-coding genes, 4 are rRNA genes, and 27 are tRNA genes. The phylogenetic result indicates B. himalaicum is sister to the genus Primula.

| S-EPMC7706784 | biostudies-literature

Lysimachia huangsangensis (Primulaceae), a New Species from Hunan, China.

Project description:A new species, Lysimachia huangsangensis (Primulaceae), from Hunan, China is described and illustrated. The new species is closely related to L. carinata because of the crested calyx, but differs in the leaf blades that are ovate to elliptic and (3-)4.5-9 × 2-3.4 cm, 2-5-flowered racemes, and the calyx lobes that are ovate-lanceolate and 5-6 × 3-4 mm. The systematic placement and conservation status are also discussed.

| S-EPMC4511667 | biostudies-literature

Lysimachia tianmaensis (Primulaceae), a new species from Anhui, China.

Project description:A new species of Lysimachia (Primulaceae), Lysimachia tianmaensis K. Liu, S.B. Zhou & Ying Wang sp. nov., is described and illustrated from Jinzhai County, Anhui, China. It is endemic to Dabieshan Mountain, China. The new species has yellow flowers and belongs to the subgenus Lysimachia section Nummularia series Grammicae. It is very easily distinguishable from other related species by having alternate leaves with brown patches beneath and an auriculated leaf base.

| S-EPMC5966504 | biostudies-literature

Complete plastid genome of Primula calliantha Franch. (Primulaceae): an alpine ornamental plant endemic to Hengduan Mountain, China.

Project description:Primula calliantha Franch. is an alpine species with an ornamental value that is endemic to the Hengduan Mountains of southwest China. Here, we sequenced and assembled its plastid complete genome, which is a circular molecule of 151,954 bp and contains a large single-copy (83,820 bp) and a small single-copy (17,814 bp) region, separated by a pair of inverted repeats (25,160 bp). There are 131 genes, 86 protein-coding, 37 tRNAs, and 8 rRNAs in the plastome, of which 114 genes, 80 CDSs, 30 tRNAs, and 4 rRNAs are unique, respectively. The P. calliantha plastid genome shows a high level of synteny with its close relatives, P. chionantha, P. purdomii, and P. woodwardii. Phylogenetic analysis based on 60 complete chloroplast genomes of Primulaceae confirmed its delimitation in Primula.

| S-EPMC8366611 | biostudies-literature

Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus.

Project description:Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36-rps8, rps16-trnQ, trnH-psbA and ndhC-trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.

| S-EPMC4928469 | biostudies-literature

Rapid detection of RNase-based self-incompatibility in Lysimachia monelli (Primulaceae).

Project description:PremisePrimroses famously employ a system that simultaneously expresses distyly and filters out self-pollen. Other species in the Primulaceae family, including Lysimachia monelli (blue pimpernel), also express self-incompatibility (SI), but involving a system with distinct features and an unknown molecular genetic basis.MethodsWe utilize a candidate-based transcriptome sequencing (RNA-seq) approach, relying on candidate T2/S-RNase Class III and S-linked F-box-motif-containing genes and harnessing the unusual evolutionary and genetic features of SI, to examine whether an RNase-based mechanism underlies SI in L. monelli. We term this approach "SI detection with RNA-seq" (SIDR).ResultsThe results of sequencing, crossing, population genetics, and molecular evolutionary features each support a causal association linking the recovered genotypes with SI phenotypes. The finding of RNase-based SI in Primulaceae (Ericales) all but cements the long-held view that this mechanism was present in the ancestral pentapetal eudicot, whose descendants now comprise two-thirds of angiosperms. It also significantly narrows the plausible maximum age for the heterostyly evolution within the family.ConclusionsSIDR is powerful, flexible, inexpensive, and most critically enables work in often-neglected species. It may be used with or without candidate genes to close enormous gaps in understanding the genetic basis of SI and the history of breeding system evolution.

| S-EPMC11744440 | biostudies-literature

Characterization of the complete plastid genome of Butia eriospatha (Arecaceae).

Project description:Butia eriospatha is an endemic palm species from the Atlantic Rainforest in Brazil, a biodiversity hotspot. This species is currently listed in the IUCN red list as vulnerable and lacks specific plastid markers for population genetics studies. In addition, the evolutionary relationship within the genus Butia is not yet well resolved. Here, we sequenced and characterized the complete plastid genome (plastome) sequence of B. eriospatha. The complete plastome sequence is 154,048 bp in length, with the typical quadripartite structure. This plastome length and genes content is consistent with other six species from tribe Cocoseae. However, the Inverted Repeat (IR) borders show some variation among the analyzed species from this tribe. Species from the Bactridinae (Astrocaryum and Acrocomia) and Elaeidinae (Elaeis) subtribes present the rps19 gene completely duplicated in the IR region. In contrast, all plastomes sequenced from the subtribe Attaleinae (Butia, Cocos, Syagrus) present one complete CDS of rps19 and one partial copy of rps19. The difference in the IR/LSC junctions between Attaleinae and the sister clades Bactridinae + Elaeidinae might be considered an evolutionary signal and the plastome sequence of B. eriopatha may be used in future studies of population genetics and phylogeny.

| S-EPMC7488953 | biostudies-literature

Plastome evolution and phylogenomic insights into the evolution of Lysimachia (Primulaceae: Myrsinoideae).

Project description:BackgroundLysimachia L., the second largest genus within the subfamily Myrsinoideae of Primulaceae, comprises approximately 250 species worldwide. China is the species diversity center of Lysimachia, containing approximately 150 species. Despite advances in the backbone phylogeny of Lysimachia, species-level relationships remain poorly understood due to limited genomic information. This study analyzed 50 complete plastomes for 46 Lysimachia species. We aimed to identify the plastome structure features and hypervariable loci of Lysimachia. Additionally, the phylogenetic relationships and phylogenetic conflict signals in Lysimachia were examined.ResultsThese fifty plastomes within Lysimachia had the typical quadripartite structure, with lengths varying from 152,691 to 155,784 bp. Plastome size was positively correlated with IR and intron length. Thirteen highly variable regions in Lysimachia plastomes were identified. Additionally, ndhB, petB and ycf2 were found to be under positive selection. Plastid ML trees and species tree strongly supported that L. maritima as sister to subg. Palladia + subg. Lysimachia (Christinae clade), while the nrDNA ML tree clearly placed L. maritima and subg. Palladia as a sister group.ConclusionsThe structures of these plastomes of Lysimachia were generally conserved, but potential plastid markers and signatures of positive selection were detected. These genomic data provided new insights into the interspecific relationships of Lysimachia, including the cytonuclear discordance of the position of L. maritima, which may be the result of ghost introgression in the past. Our findings have established a basis for further exploration of the taxonomy, phylogeny and evolutionary history within Lysimachia.

| S-EPMC10347800 | biostudies-literature

Seed germination and reproductive features of Lysimachia minoricensis (Primulaceae), a wild-extinct plant.

Project description:Lysimachia minoricensis is one of the few Mediterranean endemic plants (Minorca, Balearic islands) that has gone extinct in the wild but which persists as extant germplasm or cultivated plants in several botanical gardens. Reproductive features (seed set, number of seeds per capsule, seed weight) and germination responses to constant temperatures, sea water and dry-heat pre-treatments were investigated to determine the extent to which they may have influenced the extinction of the species. Seed set in Lysimachia is not dependent on pollinators, suggesting a functional selfer breeding system. Most plants produced a large mean number of fruits (23.2) and seeds (466), and the mean production of seeds per individual was estimated to be almost 1,100. Overall, no highly specific requirements were observed for seed germination. Seed germination was not inhibited in the dark, and a high germinability (over 87% in all cases) was recorded in most experiments, with the exception of those performed at low temperatures (5 and 10 degrees C). These data suggest that fertility and seed viability were not the major causes of extinction. The high reproductive performance of L. minoricensis is in striking contrast to its status as a wild-extinct plant, suggesting that extrinsic factors were responsible for its extinction.

| S-EPMC4233890 | biostudies-literature

Characterization of the complete plastid genome of Gaultheria griffithiana (Ericaceae).

Project description:Gaultheria griffithiana is an evergreen shrub in the family Ericaceae. It is used as a source of the Chinese traditional medicine, Tougucao, with distribution of the junction of eastern Himalaya and Hengduan Mountain. The chloroplast genome of G. griffithiana is 175,649 bp in length with 135 genes, including eight rRNA genes, 39 tRNA genes, and 85 protein-coding genes. Phylogenetic analysis has converged on the placement of G. griffithiana as sister to G. praticola, G. nummularioides, and G. hookeri within the Leucothoides clade of Gaultheria in this study.

| S-EPMC8218835 | biostudies-literature