The chromosome-level genome assembly of an endangered herb Bergenia scopulosa provides insights into local adaptation and genomic vulnerability under climate change DOI Creative Commons
Yixin Yang, Meng Wang,

Xuan-Ye Wu

et al.

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background Global climate change poses severe threats to biodiversity and ecosystem stability. Rapid oscillations potentially lead species geographic range shifts, population declines, even extinctions. The rare endangered species, being critical components of regional biodiversity, hold the key understanding local adaptation evolutionary processes shaping distributions. Therefore, assessing mechanisms vulnerability under is crucial for developing conservation strategies species. Results In this study, we assembled a high-quality, chromosome-level genome herb Bergenia scopulosa in Qinling Mountains East Asia resequenced 37 individual genomes spanning its entire distributional ranges. By integrating genetics, landscape genomics, datasets, substantial number adaptive single-nucleotide polymorphism loci associated with variables were identified. genotype–environment association analysis showed that some cold-tolerant genes have played pivotal roles cold environmental B. scopulosa. These findings are further corroborated through gene family quantitative PCR validation. Population genomic revealed 2 distinct genetic lineages western lineage higher more cold-tolerance alleles, suggesting heightened sensitivity impending should be given priority management practices. Conclusions provide novel insights into Asia. Additionally, study also offers valuable guidance formulating plants.

Language: Английский

Pangenome graphs and their applications in biodiversity genomics DOI
Simona Secomandi, Guido Roberto Gallo,

Riccardo Rossi

et al.

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

Citations

3
Grapevine pangenome facilitates trait genetics and genomic breeding DOI Creative Commons
Zhongjie Liu, Nan Wang, Ying Su

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 4, 2024

Grapevine breeding is hindered by a limited understanding of the genetic basis complex agronomic traits. This study constructs graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build variation map with 9,105,787 short variations 236,449 structural (SVs) resequencing data 466 grapevine cultivars. Integrating SVs into genome-wide association study, 148 quantitative trait loci for 29 traits (50.7% identified), 12 significantly contributed SVs. The estimated heritability improves 22.78% on average when including We discovered locus regions under divergent artificial selection in metabolism berry development between wine table grapes, respectively. Moreover, significant correlations were detected among Under polygenic model, conducted genomic predictions each trait. In general, our facilitates superior cultivars via multiple By constructing incorporating phenotypic maps, investigates traits, empowering breeding.

Language: Английский

Citations

12
DNA methylation dynamics in gymnosperm duplicate genes: implications for genome evolution and stress adaptation DOI
Kai‐Yuan Huang, Yuanyuan Feng, Hong Du

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(4)

Published: Feb. 1, 2025

SUMMARY Duplicate genes are pivotal in driving evolutionary innovation, often exhibiting expression divergence that offers a system to investigate the role of DNA methylation transcriptional regulation. However, previous studies have predominantly focused on angiosperms, leaving patterns major lineages land plants still unclear. This study explores evolution duplicate across representative gymnosperm species with large genomes, spanning over 300 million years, using genomic, transcriptomic, and high‐depth methylomic data. We observed variations levels along gene bodies, flanking regions, statuses coding regions different duplication types. Biased divergences frequently occurred between copies. Specifically, 2‐kb downstream negatively correlated expression. Both CG CHG bodies were positively length, suggesting these types may function as an epigenomic buffer mitigate adverse impact length both notably enriched adaptation‐related biological processes, aid adaptive gymnosperms by regulating stress response genes. Changes switches status within transposed duplicates. depletion for or enrichment non‐CG significantly reduced translocated correlation suggests reduce genetic redundancy silencing Our highlights significance plant genome adaptation.

Language: Английский

Citations

1
Solanum pan-genetics reveals paralogues as contingencies in crop engineering DOI Creative Commons
Matthias Benoit, Katharine M. Jenike, James W. Satterlee

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Language: Английский

Citations

1
Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations DOI Creative Commons
Yinguang Hou, Junwei Gan, Zeyu Fan

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 15, 2024

Language: Английский

Citations

5
Comparative analysis of HKTs in six poplar species and functional characterization of PyHKTs in stress-affected tissues DOI Creative Commons
Xiaojiao Liu, Lei Shi,

Huixia Bai

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 7, 2025

Abstract Plant HKTs (High-affinity K + transporters) are essential transporters for ion transport and homeostasis play crucial roles in plant growth stress responses. However, the evolution of Populus species their functions require further investigation. In this study, we identified 16 from six species. All poplar were classified as Class I because physiological relationships conservation amino acids key structures, which aligns with conserved evolutionary coding sequences. The analysis protein domains, motifs gene structures revealed consistent conservation, exception two members. number homologs chromosome locations indicated differentiation during adaptation. Poplar can be into subgroups on basis distinct structures. Gene expression pattern that presented relatively high levels roots stems under salt stress. Furthermore, cis-element interaction predictions provide insights through activation transporters, proline content, ATPases regulated by hormonal signals MYB transcription factors. conclusion, our research established a theoretical framework investigating functional offered valuable underlying mechanisms specific tissues various conditions.

Language: Английский

Citations

0
Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa DOI Creative Commons

Wentao Gao,

Sui Wang, Tao Jiang

et al.

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(4)

Published: Jan. 15, 2025

Abstract Populus trichocarpa, a pivotal model organism for woody transgenic research, not only garners substantial scientific interest but plays an integral role in forestry economics. Previous genomic assemblies of P. trichocarpa predominantly treated its heterozygous genome as homozygous, thereby neglecting crucial haplotypic diversity. Leveraging the high-fidelity (HiFi) sequencing capabilities PacBio and chromosome conformation capture insights provided by Illumina's Hi-C technique, this study is first to achieve near telomere-to-telomere assembly both paternal maternal haplotypes trichocarpa. Comparative analysis between these has uncovered several allelic variants pathways critical trait determination through allele-specific expression. Furthermore, utilizing RNA-seq data from multiple tissues, investigation detailed tissue-specific expression patterns leucine-rich repeat gene family, which are essential mediating plant signal transduction developmental regulation. Our results illuminate functional genomics landscape also provide invaluable theoretical underpinnings genetic improvement plants robust framework exploring variability disparities arboreal species.

Language: Английский

Citations

0
Developing pangenomes for large and complex plant genomes and their representation formats DOI Creative Commons

Pradeep Ruperao,

Parimalan Rangan, Trushar Shah

et al.

Journal of Advanced Research, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct comprehensive landscape, revealing both core and accessory elements. This approach enables identification novel genes, structural variations, gene presence-absence providing insights into species evolution, adaptation, trait variation. Representing requires innovative visualization formats that effectively convey complex structures variations. review delves contemporary methodologies recent advancements in constructing pangenomes, particularly plant genomes. It examines structure pangenome representation, including format comparison, conversion, techniques, their implications for enhancing crop improvement strategies. Earlier comparative have illuminated sequences, copy number variations across diverse concept pan-genome, which captures broad spectrum genotypes, offers holistic perspective species' makeup. However, pan-genome plants with larger genomes poses challenges, managing vast genome sequence comprehending germplasm. To address these researchers explored cost-effective alternatives encapsulate single known as pangenome. involves reducing volume sequences while focusing on With growing prominence genomics, several software tools emerged facilitate construction. sheds light developing utilizing tailored pan-genomes plants. also discusses representation suitable downstream analyses, offering valuable landscape evolutionary dynamics In summary, this underscores significance construction resolving architecture plants, those provides overview advancements, aiding exploring understanding diversity.

Language: Английский

Citations

0
The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems DOI Creative Commons
Yanling Peng, Yiwen Wang, Yuting Liu

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(6)

Published: Feb. 7, 2025

Hemizygous genes, which are present on only one of the two homologous chromosomes diploid organisms, have been mainly studied in context sex and sex-linked genes. However, these genes can also occur autosomes plants due to structural variants (SVs), such as a deletion/insertion allele, this phenomenon largely unexplored plants. Here, we investigated genomic epigenomic landscapes hemizygous across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples, four inbred putatively homozygous genomes. We identified SVs leading genic hemizygosity. As expected, very few (0.01 1.2%) were genomes, representing negative controls. Hemizygosity was appreciable among averaging 8.7% but consistently elevated for samples at 13.8% likely reflecting heterozygous SV accumulation during propagation. Compared more often situated centromeric than telomeric regions experienced weaker purifying selection. They had reduced levels expression, ~20% expression violating evolutionary model dosage compensation. detected higher DNA methylation transposable elements, may contribute their expression. Finally, profiles showed that specifically expressed contexts related fruit development, organ differentiation, stress responses. Overall, accumulate clonally propagated lineages display distinct genetic epigenetic features compared shedding unique insights into studies breeding programs crops.

Language: Английский

Citations

0
Comprehensive characterization of poplar HSP20 gene family: genome-wide identification, stress-induced expression profiling, and protein interaction verifications DOI Creative Commons
Lei Shi, Young-Joon Kang, Ling Ding

et al.

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 25, 2025

Heat shock proteins (HSP20s) are crucial components in plant stress responses, acting as molecular chaperones to safeguard cellular integrity and prevent abnormal protein aggregation. While extensive research has been conducted on HSP20s various species, limited information is available regarding the HSP20 family poplar (Populus yunnanensis), a species of significant ecological economic importance native southwestern China. To elucidate distribution, structural features, functional characteristics P. yunnanensis, combination bioinformatics tools experimental validation was utilized. A total 53 PyHSP20s were identified within yunnanensis genome classified into 12 subfamilies: CI, CII, CIII, CIV, CV, CVI, CVII, MI, MII, ER, CP, Px containing 24, 1, 2, 14, 3, 1 proteins, respectively. Classification based subcellular localization phylogenetic relationships, revealing subfamilies with varying exon–intron structures conserved motifs. The 3D analysis showed differentiation, CI subfamily exhibiting 8 β-sheets, compared 7 β-sheets other subfamilies. Additionally, N-terminal arms displayed heterogeneity length sequence. unevenly distributed across 15 chromosomes, tandem segmental duplications explaining expansion subfamilies, particularly CVII. cis-elements associated response hormone regulation underscored critical role PyHSP20 adaptation. Expression profiling via database qRT-PCR confirmed responsiveness multiple stressors, including salt, mannitol, drought, heat, abscisic acid (ABA). Furthermore, Yeast Two-Hybrid (Y2H) assays demonstrated potential regulatory interactions between involved responses. These findings provide comprehensive understanding classification, roles thereby establishing foundation for future investigations this family.

Language: Английский

Citations

0