Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

Chen, Tingqiao; Sun, Yue; Yuan, Tao

doi:10.1186/s12864-023-09171-1

Cited by 4 publications

(3 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Apart from the ornamental value, recent studies have also revealed the content of abundant unsaturated fatty acids in seeds and potential medical compounds in the roots and seeds of P. ludlowii and other peony species [ 3 , 5 , 19 ]. In addition, some studies on P. ludlowii have focused on seed biology, like endosperm abortion or seed abortion, as the natural reproduction of P. ludlowii is limited due to its low fecundity [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

High-quality assembly and methylome of a Tibetan wild tree peony genome (Paeonia ludlowii) reveal the evolution of giant genome architecture

Xiao,

Li,

et al. 2023

Horticulture Research

View full text Add to dashboard Cite

Tree peony belongs to one of Saxifragales families, Paeoniaceae. It is one of the most famous ornamental plants, also becomes one promising woody oil plants. Although two Paeoniaceae genomes have been released, their assembly qualities are still to be improved. Additionally, more genomes from wild peonies are needed to accelerate genomic-assisted breeding. Here we assemble a high-quality and chromosome-scale 10.3 Gb genome of a wild Tibetan tree peony (Paeonia ludlowii), which features substantial sequence divergence, including around 75% specific sequences and gene-level differentials compared to other peony genomes. Our phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa, and together with Rosids, they are the sister taxon to Asterids. The P. ludlowii genome is characterized by frequent chromosome reductions, centromere rearrangements, broadly distributed heterochromatin, and recent continuous bursts of transposable elements (TEs) movement in peony, although it lacks recent whole genome duplication. These recent TE bursts appeared during the uplift and glacial period of the Qinghai-Tibet Plateau, perhaps contributing to adaptation to rapid climate changes. Further integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation, TE removal, and DNA methylation silencing. Such interactions also impact numerous recently duplicated genes, particularly those related to oil biosynthesis and flower traits. This genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study for the evolution of huge genome structures as well as their protein-coding genes.

show abstract

Section: Introductionmentioning

confidence: 99%

High-quality assembly and methylome of a Tibetan wild tree peony genome (Paeonia ludlowii) reveal the evolution of giant genome architecture

Xiao,

Li,

et al. 2023

Horticulture Research

View full text Add to dashboard Cite

show abstract

“…Currently, the population of P. ludlowii is declining, and is largely sustained by elderly individuals ( Yang et al., 2007 ). Recent studies have revealed that the abortion of P. ludlowii occurs during the process of double fertilization and ovule development, and its low seed-setting rate is a key limiting factor for the expansion of wild populations, as well as introduction and cultivation efforts ( Chen et al., 2022 ; Chen et al., 2023 ).Since the late 20th century, regions in China including Shandong, Henan, and Beijing have attempted to introduce and cultivate P. ludlowii , however, most areas experienced plant death after introduction, failed to bloom, or exhibited rare and unstable flowering stages. As of now, only a few regions, such as Luoyang Paeoniaceae Ex-situ Protection Center in Henan Province (Luanchuan), Gansu Provincial Forestry Science and Technology Extension Station (Lanzhou), and Vegetable Research Institute of Agriculture and Animal Husbandry College of Tibet Autonomous Region (Lhasa), have successfully introduced varieties that can bloom and bear fruit under normal circumstances ( Ni, 2009 ; Li et al., 2011 ; Cui et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Differences in rhizosphere soil fungal communities of wild and cultivated Paeonia ludlowii species

Qiao,

Gao,

Yuan

2023

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…With the gradual development of sequencing technology and decreasing cost, transcriptome sequencing technology has been applied to plant breeding, stress, genetic analysis, etc. (25)(26)(27). Lipopolysaccharide, a pro-inflammatory compound from the outer walls of Gram-negative bacteria, promotes intestinal inflammation.…”

Section: Introductionmentioning

confidence: 99%

The transcriptome sequencing analysis reveals immune mechanisms of soybean fermented powder on the loach (Misgurnus anguillicaudatus) in response to Lipopolysaccharide (LPS) infection

Xu,

Zhang,

et al. 2023

Front. Immunol.

View full text Add to dashboard Cite

The loach (Misgurnus anguillicaudatus), a small commercial fish that is widely cultivated for its high-quality protein, vitamins, minerals, and essential amino acid, is a member of the genus Misgurnus and the family Cyprinidae. In this study, we gave the LPS-injected loach fermented soybean meal and used transcriptome sequencing to investigate the impact of the fermented soybean powder on the loach’s immune system. 3384 up-regulated genes and 12116 down-regulated genes were found among the 15500 differentially expressed genes, according to the results. The differentially expressed genes were shown to be involved in cellular processes, metabolic processes, cellular anatomical entities, and binding, according to the Go functional annotation. Meanwhile, the KEGG enrichment analysis indicated that the soybean fermented powder treated groups showed significant differences in DNA replication, Nucleotide excision repair, Fanconi anemia pathway, and Base excision repair pathways, suggesting that these pathways are closely related to the enhancement of the immune function of loach by soybean fermented powder. The particular conclusions not exclusively can provide a new conception for the rational utilization of soybean fermented powder but also can provide theoretical guidance for the subsequent healthy breeding of loach.

show abstract

Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

Cited by 4 publications

References 64 publications

High-quality assembly and methylome of a Tibetan wild tree peony genome (Paeonia ludlowii) reveal the evolution of giant genome architecture

High-quality assembly and methylome of a Tibetan wild tree peony genome (Paeonia ludlowii) reveal the evolution of giant genome architecture

Differences in rhizosphere soil fungal communities of wild and cultivated Paeonia ludlowii species

The transcriptome sequencing analysis reveals immune mechanisms of soybean fermented powder on the loach (Misgurnus anguillicaudatus) in response to Lipopolysaccharide (LPS) infection

Contact Info

Product

Resources

About