Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Complete Genome Sequence of Ginkgo biloba (Ginkgoaceae, Ginkgoales), the Maidenhair Tree.

ABSTRACT: Ginkgo biloba is the only extant member of the order Ginkgoales. Fossils similar to this species extend back to the Middle Jurassic approximately 170 million years ago. Ginkgo trees are native to deciduous forests in China but are cultivated throughout North America, Europe, and Asia. We present the whole genome sequence of this species. Illumina sequencing was performed on a leaf tissue sample from a single cultivated plant. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR22349630) and Genome Assembly (JANKJI000000000).

SUBMITTER: Habib N

PROVIDER: S-EPMC9731352 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The Complete Genome Sequence of Ginkgo biloba (Ginkgoaceae, Ginkgoales), the Maidenhair Tree.

Habib Nihal N Pirro Stacy S Ghazal Hassan H

Biodiversity genomes 20221101

Ginkgo biloba is the only extant member of the order Ginkgoales. Fossils similar to this species extend back to the Middle Jurassic approximately 170 million years ago. Ginkgo trees are native to deciduous forests in China but are cultivated throughout North America, Europe, and Asia. We present the whole genome sequence of this species. Illumina sequencing was performed on a leaf tissue sample from a single cultivated plant. The reads were assembled using a de novo method followed by a s ...[more]

PMID: 36506715

Similar Datasets

The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction.

Project description:We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), the only relict of ginkgophytes from the Triassic Period. The cpDNA molecule of ginkgo is quadripartite and circular, with a length of 156,945 bp, which is 6,458 bp shorter than that of Cycas taitungensis. In ginkgo cpDNA, rpl23 becomes pseudo, only one copy of ycf2 is retained, and there are at least five editing sites. We propose that the retained ycf2 is a duplicate of the ancestral ycf2, and the ancestral one has been lost from the inverted repeat A (IR(A)). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants.

| S-EPMC3318433 | biostudies-literature

Draft genome of the living fossil Ginkgo biloba.

Project description:BackgroundGinkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution.FindingsThe 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways.ConclusionsThe ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.

| S-EPMC5118899 | biostudies-literature

Vibration responses characteristics of a Ginkgo biloba tree excited under harmonic excitation.

Project description:The most effective method of the fruit harvesting is the mechanical harvest. The frequency spectrum of different testing positions on a Ginkgo biloba tree under the impact excitation was tested in the laboratory. The acceleration responses under the harmonic excitation were measured at the frequency of the peak and trough points in the frequency spectrum curves. Results of this research indicate that the frequency spectrum presented the consistency on the same branch but distinction among different branches. There was a correspondence between the frequency spectrum characteristics and the vibration responses. The vibration responses could be strengthened at the resonant frequency. Merely, the acceleration responses at low frequency were very weak. At higher frequency, the vibration responses were strong but presented different characteristics among different branches. The acceleration response on the trunk was always the weakest. On the same branch, the dynamic responses presented the similar characteristics and the acceleration amplitude increased gradually as the testing position was located away from the excitation point on the trunk. Among different branches, the strongest dynamic response appeared at different frequencies. Our results indicate that it was difficult to induce the strong vibration response of all the branches at the single frequency during the practical mechanical harvesting of fruits.

| S-EPMC8378724 | biostudies-literature

Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba.

Project description:The complete and unambiguous (1)H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive (1)H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d(6) were obtained through the examination of 1D (1)H NMR and 2D (1)H,(1)H-COSY data, in combination with (1)H iterative full spin analysis (HiFSA). The computational analysis of discrete spin systems allowed a detailed characterization of all the (1)H NMR signals in terms of chemical shifts (δ(H)) and spin-spin coupling constants (J(HH)), regardless of signal overlap and higher order coupling effects. The capability of the HiFSA-generated (1)H fingerprints to reproduce experimental (1)H NMR spectra at different field strengths was also evaluated. As a result of this analysis, a revised set of (1)H NMR parameters for all ten phytoconstituents was assembled. Furthermore, precise (1)H NMR assignments of the sugar moieties of isoquercetin and rutin are reported for the first time.

| S-EPMC3590027 | biostudies-literature

The complete plastid genome provides insight into maternal plastid inheritance mode of the living fossil plant Ginkgo biloba.

Project description:In the current research, we focus on uniparental inheritance of chloroplast genome of the living fossil plant, Ginkgo biloba L., one of the gymnosperms, using genomic data.•Our results provide strong genomic evidence to support plastid maternal inheritance mode of G. biloba, which is different from most other gymnosperms.•The combination of manually genetic crosses and genomic data is proved to be an efficient way to investigate the inheritance mode of chloroplasts genome in land plants.•The current research also provides a case study for further research of plastid inheritance in gymnosperms using genomic techniques, which will contribute to a better understanding of cytologically uniparental inheritance mode and evolutionary mechanism of plastids in both gymnosperms and angiosperms.

| S-EPMC10772217 | biostudies-literature

GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba.

Project description:Although an increasing number of species-specific databases have been constructed to facilitate the global research community, comprehensive databases remain rare with multidimensional research resources rather than genomic data solely, in particular for non-model species. Here we introduced GinkgoDB, the ecological genome database for the world-renowned living fossil, Ginkgo biloba L., a tree species with extreme longevity, exceptional resistance, global landscape application and dioecy. The present version of GinkgoDB consists of four modules of genome, occurrence, quadrat and gallery. The genome module includes two versions of chromosome-level assembled genomes with high-quality annotation, expression profiles of each sex for different tissues and variants from 545 ginkgo genomes. A suite of tools were also deployed online for search, blast and further analyses. The occurrence module contains distribution information of over one million records across the world with an emphasis on 8926 individual-level tagged trees with phenotypic trait data in eastern Asia. The quadrat module provides monitoring data of both species and habitats from 27 plots of natural ginkgo forests and periodic data of functional traits measured for the entire plant communities. The gallery module collects field morphological photos and scanned phenotypic images of various ginkgo materials. GinkgoDB showcases a comprehensive and persistently growing database for a single non-model species. Database URL: https://ginkgo.zju.edu.cn/.

| S-EPMC9235008 | biostudies-literature

Characterization of the complete chloroplast genome of Ginkgo biloba L. (Ginkgoaceae), an endangered species endemic to China.

Project description:Ginkgo biloba L. is the oldest relict plant among the gymnosperms, left after the quaternary glacial movement. There are few living G. biloba and few old trees over a hundred years old. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of G. biloba L. by Illumina paired-end reads data. The whole genome was 156,988 bp, consisting of a pair of inverted repeats of 34,056 bp, large and small single copy regions of 56,819 and 22,763 bp in length, respectively. The cp genome contained 131 genes, including 84 protein-coding genes, 31 trRNA genes and 5 rRNA genes. The overall GC content of the whole genome was 39.6%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between G. biloba L. and Cycas revoluta.

| S-EPMC7707647 | biostudies-literature