Paeonia ludlowii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA600148 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10874392.fastq.gz | Fastqsanger.gz |
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Project description:Paeonia ludlowii Genome sequencing and assembly
| PRJNA818047 | ENA
Project description:BackgroundPaeonia ludlowii (Stern & G. Taylor D.Y. Hong) belongs to the peony group of the genus Paeonia in the Paeoniaceae family and is now classified as a "critically endangered species" in China. Reproduction is important for this species, and its low fruiting rate has become a critical factor limiting both the expansion of its wild population and its domestic cultivation.ResultsIn this study, we investigated possible causes of the low fruiting rate and ovule abortion in Paeonia ludlowii. We clarified the characteristics of ovule abortion and the specific time of abortion in Paeonia ludlowii, and used transcriptome sequencing to investigate the mechanism of abortion of ovules in Paeonia ludlowii.ConclusionsIn this paper, the ovule abortion characteristics of Paeonia ludlowii were systematically studied for the first time and provide a theoretical basis for the optimal breeding and future cultivation of Paeonia ludlowii.
| S-EPMC9936667 | biostudies-literature
Project description:IntroductionPaeonia ludlowii is a rare and endangered plant species with a high application value. However, its low cultivation success rate in China has severely limited its protection, development, and utilization. In addition to natural factors, microorganisms in the rhizosphere play an important role in determining its cultivation success.MethodsIn this study, growth indexes and soil physicochemical properties of both wild (origin: Nyingchi) and cultivated (introduction: Luanchuan) species of P. ludlowii were measured during the flowering, fruiting, and autumn foliage stages. ITS high-throughput sequencing technology was employed to detect rhizosphere soil fungi, and the diversity, community structure, functional prediction, molecular network, and ecological processes of the microbial community assembly were examined by multidirectional analysis.Results and discussionThe results indicated that: both wild and cultivated P. ludlowii species were able to flower and fruit normally, although the wild species had a higher number of flowers and fruits and higher soil available phosphorus and available potassium contents than those of the cultivated species. Ascomycota and Basidiomycota were the dominant rhizosphere soil fungal phyla in both P. ludlowii species. However, our network analysis showed that Ascomycota as the key fungal phylum of the wild species, whereas the cultivated species lacked key fungi. The community assembly mechanisms of rhizosphere soil fungi in both wild and cultivated species were primarily stochasticity, with no significant differences between them. Based on the results of FUNGuild and molecular network analyses, cultivated species had a higher proportion of fungi, such as Soil Saprotroph, that can easily cause diseases. Additionally, the network connections among fungi were weaker in the cultivated species than those in the wild species, which increased the cultivated species susceptibility to external environmental interferences. Therefore, from a soil microorganism perspective, this study suggests that, after the introduction and cultivation of P. ludlowii, if rhizosphere soil fungi fail to gradually form a close network relationship and instead promote the growth of pathogenic fungi, the fungal ecosystem would become vulnerable.
| S-EPMC10520497 | biostudies-literature
Project description:Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of the endophytic bacterial communities associated with different tissues, including fruits, flowers, leaves, stems, and roots, and rhizosphere soils was analyzed with Illumina MiSeq sequencing of bacterial 16S rDNA. A total of 426,240 sequences and 4847 operational taxonomic units (OTUs) were obtained. The OTUs abundance of roots was higher than that of other tissues; however, the OTUs abundance was similar among different deep soil samples. In the plant tissues, Cyanobacteria was the most abundant bacterial phylum, followed by Proteobacteria; however, the most abundant phyla were Proteobacteria and Acidobacteria in soil samples from three different layers. In addition, the diversity and richness of the microorganisms in the soil were very similar to those in roots but higher than those in other tissues of P. ludlowii. Predictive metagenome analysis revealed that endophytic bacteria play critical functional roles in P. ludlowii. This conclusion could facilitate the study of the ecological functions of endophytic bacteria and their interactions with P. ludlowii to analyze the reasons why this important medicinal plant is becoming endangered.
| S-EPMC7385006 | biostudies-literature
Project description:Himalaya and Hengduan Mountains (HHM) is a biodiversity hotspot, and very rich in endemic species. Previous phylogeographical studies proposed different hypotheses (vicariance and climate-driven speciation) in explaining diversification and the observed pattern of extant biodiversity, but it is likely that taxa are forming in this area in species-specific ways. Here, we reexplored the phylogenetic relationship and tested the corresponding hypotheses within Paeonia subsect. Delavayanae composed of one widespread species (Paeonia delavayi) and the other geographically confined species (Paeonia ludlowii). We gathered genetic variation data at three chloroplast DNA fragments and one nuclear gene from 335 individuals of 34 populations sampled from HHM. We performed a combination of population genetic summary statistics, isolation-with-migration divergence models, isolation by environment, and demographic history analyses. We found evidence for the current taxonomic treatment that P. ludlowii and P. delavayi are two different species with significant genetic differentiation. The significant isolation by environment was revealed within all sampled populations but genetic distances only explained by geographical distances within P. delavayi populations. The results of population divergence models and demographic history analyses indicated a progenitor-derivative relationship and the Late Quaternary divergence without gene flow between them. The coalescence of all sampled cpDNA haplotypes could date to the Late Miocene, and P. delavayi populations probably underwent a severe bottleneck in population size during the last glacial period. Genetic variation in Paeonia subsect. Delavayanae is associated with geographical and environmental distances. These findings point to the importance of geological and climatic changes as causes of the speciation event and lineage diversification within Paeonia subsect. Delavayanae.
| S-EPMC7874331 | biostudies-literature
Project description:Compared with traditional genetic markers, genomic approaches have proved valuable to the conservation of endangered species. Paeonia ludlowii having rarely and pure yellow flowers, is one of the world's most famous tree peonies. However, only several wild populations remain in the Yarlung Zangbo Valley (Nyingchi and Shannan regions, Xizang) in China due to increasing anthropogenic impact on the natural habitats. We used genome-wide single nucleotide polymorphisms to elucidate the spatial pattern of genetic variation, population structure and demographic history of P. ludlowii from the fragmented region comprising the entire range of this species, aiming to provide a basis for conserving the genetic resources of this species. Unlike genetic uniformity among populations revealed in previous studies, we found low but varied levels of intra-population genetic diversity, in which lower genetic diversity was detected in the population in Shannan region compared to those in Nyingzhi region. These spatial patterns may be likely associated with different population sizes caused by micro-environment differences in these two regions. Additionally, low genetic differentiation among populations (Fst = 0.0037) were detected at the species level. This line of evidence, combined with the result of significant genetic differentiation between the two closest populations and lack of isolation by distance, suggested that shared ancestry among now remnant populations rather than contemporary genetic connectivity resulted in subtle population structure. Demographic inference suggested that P. ludlowii probably experienced a temporal history of sharp population decline during the period of Last Glacial Maximum, and a subsequent bottleneck event resulting from prehistoric human activities on the Qinghai-Tibet Plateau. All these events, together with current habitat fragment and excavation might contribute to the endangered status of P. ludlowii. Our study improved the genetic characterization of the endangered tree peony (P. ludlowii) in China, and these genetic inferences should be considered when making different in situ and ex situ conservation actions for P. ludlowii in this evolutionary hotspot region.
| S-EPMC10625974 | biostudies-literature