Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids DOI Open Access
Luxian Liu, Mengzhen Chen, Ryan A. Folk

et al.

Authorea (Authorea), Journal Year: 2023, Volume and Issue: unknown

Published: March 11, 2023

Some of the most vexing problems deep level relationship that remain in angiosperms involve superrosids. The superrosid clade contains a quarter all angiosperm species, with 18 orders three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological ecological diversity. To help resolve deep-level relationships, we constructed high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation Saxifragales. Whole microsynteny analysis superrosids showed shared more synteny clusters rosids than Vitales, further supporting as closely related rosids. ordinal phylogeny superrosids, screened 122 single copy nuclear genes from genomes 36 representing orders. Vitales were recovered sister to other (Saxifragales + rosids). Our data suggest dramatic differences relationships compared earlier studies within Fabids should be restricted nitrogen-fixing clade, while Picramniales, Celastrales-Malpighiales (CM) Huerteales, Oxalidales, Sapindales, Malvales Brassicales formed an “expanded” malvid clade. Celastrales-Oxalidales-Malpighiales (COM) (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales Zygophyllales did belong either our well-supported malvids or fabids. There is strong discordance between plastid phylogenetic hypotheses relationships; show this best explained by combination incomplete lineage sorting ancient reticulation.

Language: Английский

Rosaceae phylogenomic studies provide insights into the evolution of new genes DOI Creative Commons
Lan Jiang,

Xiaoxu Li,

Kun Lyu

et al.

Horticultural Plant Journal, Journal Year: 2024, Volume and Issue: unknown

Published: May 1, 2024

Rosa banksiae, known as Lady Banks' rose, is a perennial ornamental crop and versatile herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled HiFi Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R. banksiae genome with scaffold N50 = 63.90 Mb. The exhibited no lineage-specific whole-genome duplication compared other Rosaceae. phylogenomic analysis 13 Rosaceae Arabidopsis through comparative genomics study showed that numerous gene families were both before after diversification Some these genes are candidates for new have evolved from parental fusion events. Fusion divided into three types: Type-I Type-II contain two generated by duplication, distributed same different regions genome, respectively; Type-III can only be detected one gene. Here, found to more relaxed selection pressure lower Ks values than Type-II, indicating newly may play important roles driving phenotypic evolution. Functional formed regulate phenotype traits plant growth development, suggesting functional significance genes. This identifies could responsible evolution provides information on evolutionary history recently diverged species genus. Our data represents major progress understanding pattern an invaluable resource studies plants.

Language: Английский

Citations

16
Preservation effects of chitosan/polyvinyl alcohol/clove essential oil antifungal film on yellow peaches: Physicochemical properties and fruit quality assessment DOI
Liyuan Wang,

Hongjun Fu,

Qian Tan

et al.

Food Control, Journal Year: 2024, Volume and Issue: 164, P. 110582 - 110582

Published: May 11, 2024

Language: Английский

Citations

14
Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt DOI Creative Commons
Yunpeng Cao,

Wanzhen Mo,

Yanli Li

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Feb. 27, 2024

Abstract Background Most disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii its resistant counterpart, montana , offer significant resources for functional characterization discovery novel tung tree. Results Here, we identified 239 across two tree genomes: 90 V. 149 . Five VmNBS-LRR paralogous were predicted 43 orthologous detected between gene pair Vf11G0978-Vm019719 exhibited distinct expression patterns : Vf11G0978 showed downregulated while Vm019719 demonstrated upregulated indicating this may be responsible wilt from activated by VmWRKY64 was shown confer a virus-induced silencing (VIGS) experiment. However, susceptible allelic an ineffective defense response, attributed deletion promoter’s W-box element. Conclusions This study provides first systematic analysis identifies candidate can utilized marker-assisted breeding control

Language: Английский

Citations

13
De novo gene integration into regulation networks via interaction with conserved genes in peach DOI Creative Commons
Yunpeng Cao,

Jiayi Hong,

Yun Zhao

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(12)

Published: Sept. 5, 2024

Language: Английский

Citations

12
Population sequencing of cherry accessions unravels the evolution of Cerasus species and the selection of genetic characteristics in edible cherries DOI Creative Commons

Yahui Lei,

Songtao Jiu, Yan Xu

et al.

Molecular Horticulture, Journal Year: 2025, Volume and Issue: 5(1)

Published: Jan. 8, 2025

Abstract Cerasus is a subgenus of Prunus in the family Rosaceae that popular owing to its ornamental, edible, and medicinal properties. Understanding evolution identifying selective trait loci edible cherries are crucial for improvement cherry cultivars meet producer consumer demands. In this study, we performed de novo assembly chromosome-scale genome sweet ( avium L . ) cultivar ‘Burlat’, covering 297.55 Mb consisting eight chromosomes with 33,756 protein-coding genes. The resequencing population structural analysis 384 representative accessions revealed they could be divided into four groups (Group 1, Group 2, 3, 4). We inferred 1 was oldest Groups 4 were clades derived from it. addition, found sweeps fruit flavor improved stress resistance different varieties P. , cerasus pseudocerasus Transcriptome significant differential expression genes associated key pathways, such as sucrose starch metabolism, fructose mannose pentose phosphate pathway, between leaves fruits This study enhances understanding evolutionary processes provides resources functional genomics research cherries.

Language: Английский

Citations

1
Adaptation of High-Altitude Plants to Plateau Abiotic Stresses: A Case Study of the Qinghai-Tibet Plateau DOI Open Access
Pengcheng Sun,

Ruirui Hao,

Fangjing Fan

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 2292 - 2292

Published: March 4, 2025

High-altitude regions offer outstanding opportunities for investigating the impacts of combined abiotic stresses on plant physiological processes given their significant differences in terms ecological environment high-elevation areas, low anthropogenic disturbance, and obvious distribution characteristics plants along altitudinal gradients. Therefore, high-altitude areas can be used as good targets exploring adaptations to stress under extreme conditions. Plants that thrive environments such Qinghai-Tibet Plateau endure stresses, including temperatures, high UV radiation, nutrient-poor soils. This study explores adaptation mechanisms via phenotypic variation analyses multiomics approaches. Key findings highlight traits increased photosynthetic efficiency, robust antioxidant systems, morphological modifications tailored These insights advance our understanding evolution harsh inform strategies increase resistance crops.

Language: Английский

Citations

1
Smart breeding driven by advances in sequencing technology DOI Creative Commons

Chenji Zhang,

Sirong Jiang, Yangyang Tian

et al.

Modern Agriculture, Journal Year: 2023, Volume and Issue: 1(1), P. 43 - 56

Published: March 1, 2023

Abstract Crop breeding has undergone numerous advancements throughout history with the next revolution being uncertain. This review provides an overview of techniques from traditional selective and crossbreeding to modern based on molecular marker‐assisted genomic selection. Systematic analysis mainstream genotyping approaches principle, application scenario supporting software revealed that changes in technology have led explosion data. data expansion will drive a breakthrough sequencing integrate artificial intelligence automation. The also discusses technological associated during big era, including models, technologies future intelligent breeding, provide references for crop breeders. paper highlights potential smart driven by advances technology, which lead development new strategies accelerate process.

Language: Английский

Citations

15
Genomic insights into domestication and genetic improvement of fruit crops DOI Open Access
Runze Wang, Xiaolong Li, Minzhang Sun

et al.

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 192(4), P. 2604 - 2627

Published: May 10, 2023

Abstract Fruit crops cultivated in almost all countries and regions around the world serve as important agricultural commodities of significant economic value because they contribute to overall food security by providing a diverse nutrient supply sustain human life health. Recent advances high-throughput sequencing technologies offer unprecedented opportunities for pursuing genomic genetic studies fruit crops. Here, we will review major crop genome efforts undertaken over past 15 years that have contributed accumulation publicly available resources. We highlight expanding pool data better unravel origin domestication trees, well deciphering genetics horticultural traits these trees. Furthermore, explore how utilization features trees along with new genomic-assisted tools, including selection gene editing, are informing guiding plant geneticists breeders moving forward their breeding efforts. Finally, outline future prospects unresolved questions remain both research improvement

Language: Английский

Citations

15
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids DOI Open Access
Luxian Liu, Mengzhen Chen, Ryan A. Folk

et al.

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(7), P. 1673 - 1688

Published: July 14, 2023

Some of the most vexing problems deep level relationship that remain in angiosperms involve superrosids. The superrosid clade contains a quarter all angiosperm species, with 18 orders three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological ecological diversity. To help resolve deep-level relationships, we constructed high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation Saxifragales. Whole microsynteny analysis superrosids showed shared more synteny clusters rosids than Vitales, further supporting as closely related rosids. ordinal phylogeny superrosids, screened 122 single copy nuclear genes from genomes 36 representing orders. Vitales were recovered sister to other (Saxifragales + rosids). Our data suggest dramatic differences relationships compared earlier studies within Fabids should be restricted nitrogen-fixing clade, while Picramniales, Celastrales-Malpighiales (CM) Huerteales, Oxalidales, Sapindales, Malvales Brassicales formed an "expanded" malvid clade. Celastrales-Oxalidales-Malpighiales (COM) (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales Zygophyllales did belong either our well-supported malvids or fabids. There is strong discordance between plastid phylogenetic hypotheses relationships; show this best explained by combination incomplete lineage sorting ancient reticulation.

Language: Английский

Citations

13
The snapdragon genomes reveal the evolutionary dynamics of the S locus supergene DOI Creative Commons
Sihui Zhu, Yu’e Zhang,

Lucy Copsy

et al.

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(4)

Published: April 1, 2023

The genus Antirrhinum has been used as a model to study self-incompatibility extensively. multi-allelic S-locus, carrying pistil S-RNase and dozens of S-locus F-box (SLF) genes, underlies the genetic control (SI) in hispanicum. However, there have limited studies on genomic organization supergene due lack high-quality data. Here, we present chromosome-level reference haplotype-resolved genome assemblies self-incompatible A. hispanicum line, AhS7S8. For first time, 2 complete S-haplotypes spanning ∼1.2 Mb containing total 32 SLFs were reconstructed, whereas most derived from retroelement-mediated proximal or tandem duplication ∼122 Mya. Back then, gene incipient came into linkage form pro-type type-1 common ancestor eudicots. Furthermore, detected pleiotropic cis-transcription factor (TF) associated with regulating expression SLFs, two miRNAs may this TF. Interspecific intraspecific S-haplotype comparisons revealed dynamic nature polymorphism mediated by continuous duplication, segmental translocation loss, TE-mediated transposition events. Our data provide an excellent resource for future research evolutionary S-RNase-based system.

Language: Английский

Citations

10