Different Genotypes of the Rare and Threatened Moss Physcomitrium eurystomum (Funariaceae) Exhibit Different Resilience to Zinc and Copper Stress DOI Creative Commons
Djordje P. Božović, Marija V. Ćosić, Vladislav Kolarčik

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(2), P. 224 - 224

Published: Jan. 15, 2025

The funarioid moss species Physcomitrium eurystomum, which is threatened with extinction, was the subject of this study. riparian habitat type often under influence contaminated water, and, therefore, we tested selected potentially toxic elements (PTEs), namely zinc and copper, on development, physiological features, survival two different accessions (German Croatian). results obtained showed resilience to PTEs. Flow cytometry analyses revealed that differ significantly in terms genome size. However, amplitude PTEs, divergence responses, within same are confirmed, as well dissimilarity their size, likely associated ploidy level difference possibly distinct hybrid origin.

Language: Английский

TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining DOI Creative Commons
Chengjie Chen,

Ya Wu,

Jiawei Li

et al.

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(11), P. 1733 - 1742

Published: Sept. 22, 2023

Language: Английский

Citations

1284
Technology-enabled great leap in deciphering plant genomes DOI
Lingjuan Xie, Xiaojiao Gong, Kun Yang

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: 10(4), P. 551 - 566

Published: March 20, 2024

Language: Английский

Citations

32
Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice DOI Creative Commons
Hua Wei, Xianmeng Wang, Zhipeng Zhang

et al.

National Science Review, Journal Year: 2024, Volume and Issue: 11(4)

Published: Feb. 5, 2024

ABSTRACT For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing response salt remains limited natural germplasm. Through transcriptome analysis the Global Mini-Core Rice Collection consisting panel 202 accessions, we identified 22 345 and 27 610 quantitative trait loci associated with 7787 9361 eGenes under normal salt-stress conditions, respectively, leveraging super pan-genome map. Notably, combined genome-wide association studies, swiftly pinpointed potential candidate STG5—a major salt-tolerant locus known as qSTS5. Intriguingly, STG5 is required for maintaining Na+/K+ homeostasis directly regulating transcription multiple members OsHKT family. Our study sheds light on how variants influence dynamic changes provides valuable resource mining genes future.

Language: Английский

Citations

17
Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis DOI Creative Commons
Weikai Chen, Xiangfeng Wang, Jie Sun

et al.

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

Published: May 20, 2024

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history capsaicinoid biosynthesis and mechanism their tissue specificity remain obscure lack high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes C. annuum wild nonpungent relative rhomboideum investigate evolution in chili peppers. We precisely delineate centromeres, which high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, estimate timing biosynthesis. reveal disrupted coding regulatory regions key genes species. also find conserved placenta-specific accessible chromatin regions, likely allow tissue-specific biosynthetic gene coregulation accumulation. These T2T genomic resources will accelerate genetic improvement help understand genome evolution.

Language: Английский

Citations

15
Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape DOI Creative Commons
Tianhao Zhang,

Wenjing Peng,

Hua Xiao

et al.

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(7), P. 1408 - 1426

Published: April 5, 2024

ABSTRACT Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on phenotypic traits and local adaptation to abiotic biotic stress. In this study, we employed woolly grape ( Vitis retordii ), species native the tropical subtropical regions East Asia with both coastal inland habitats, as valuable model for examining SVs adaptation. We assembled haplotype‐resolved chromosomal reference genome grape, conducted population genetic analyses based whole‐genome sequencing (WGS) data from populations. The demographic revealed recent bottlenecks in all populations asymmetric gene flow population. total, 1,035 genes associated adaptive regulation salt stress, radiation, environmental were detected underlying selection by SNPs population, which 37.29% 65.26% SNPs, respectively. Candidate such FSD2 , RGA1 AAP8 tolerance found be highly differentiated selected during process habitats SV regions. Our study highlights importance adaptation; candidate related stress climatic environments important genomic resources future breeding programs grapevine its rootstocks.

Language: Английский

Citations

12
A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice DOI Creative Commons
Xiaoxia Li,

Xiaofan Dai,

Huiying He

et al.

National Science Review, Journal Year: 2024, Volume and Issue: 11(6)

Published: May 3, 2024

Transposable elements (TEs) are ubiquitous genomic components and hard to study due being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the with 15 existing assemblies, developed a pan-TE map comprising both cultivated wild Asian rice. We detected 177 084 high-quality TE variations inferred their derived state using outgroups. found TEs were one source of phenotypic variation during rice domestication differentiation. identified 1246 genes whose expression was associated but not single-nucleotide polymorphisms (SNPs), such as

Language: Английский

Citations

9
Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication DOI Creative Commons
Ying Su,

X Yang,

Y. Wang

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(4), P. 2799 - 2814

Published: May 14, 2024

Abstract The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies breeding programs. In this study, we assembled haplotype-resolved telomere-to-telomere (T2T) genome for diploid cultivar Golden Delicious. Subsequently, constructed pangenome based on 12 assemblies from wild species to investigate dynamic changes functional genes. Our results revealed gene gain loss events during domestication. Compared with species, more families significantly enriched oxidative phosphorylation, pentose metabolic process, responses salt, abscisic acid biosynthesis process. analyses also demonstrated higher prevalence different types resistance analogs (RGAs) cultivars than their relatives, partially attributed segmental tandem duplication certain RGAs classes. Structural variations, mainly deletions insertions, have affected presence absence TIR-NB-ARC-LRR, NB-ARC-LRR, CC-NB-ARC-LRR Additionally, hybridization/introgression has contributed expansion genes domesticated apples. T2T provide important resources apples, emphasizing need study evolutionary mechanisms breeding.

Language: Английский

Citations

8
Harnessing genomic and molecular biology resources for genetic improvement of lotus: current achievements and future directions DOI Creative Commons
Heng Sun, Xin Jia,

Heyun Song

et al.

Horticulture Advances, Journal Year: 2025, Volume and Issue: 3(1)

Published: Jan. 10, 2025

Abstract Lotus, an economically significant aquatic crop within the genus Nelumbo (family naceae), includes two extant species nucifera and lutea . Renowned for its ornamental, culinary, medicinal value, lotus has seen notable advancements in genomics molecular biology, particularly reference genome sequencing assembly, bioactive compound biosynthetic pathways, mechanisms underlying key traits. Critical genes linked to horticultural characteristics, edible quality, properties, stress resilience have been identified functionally validated. This review presents a thorough overview of recent developments research, emphasizing functional gene analysis. Additionally, it addresses prevailing challenges future directions, providing valuable insights foundational research genetic enhancement lotus.

Language: Английский

Citations

1
A simple and efficient TALEN system for genome editing in plants DOI
Qing Liu,

Lei Lin,

Shunmin He

et al.

Plant Molecular Biology, Journal Year: 2025, Volume and Issue: 115(1)

Published: Jan. 21, 2025

Language: Английский

Citations

1
A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants DOI Creative Commons
Tianyi Wang, Wenchuang He, Xiaoxia Li

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(20), P. 10924 - 10933

Published: Oct. 16, 2023

Detailed knowledge of the genetic variations in diverse crop populations forms basis for improvement and gene functional studies. In present study, we analyzed a large rice population with total 10 548 accessions to construct super-population variation map (RSPVM), consisting 54 378 986 single nucleotide polymorphisms, 11 119 947 insertion/deletion mutations 184 736 presence/absence variations. Assessment detection efficiency different sizes revealed sharp increase all types as size increased gradual saturation that after reached 000. Variant frequency analysis indicated ∼90% obtained variants were rare, would therefore likely be difficult detect relatively small population. Among rare variants, only 2.7% predicted deleterious. Population structure, diversity polymorphism this evaluated based on subsets RSPVM, demonstrating great potential RSPVM use downstream applications. Our study provides both rich understanding natural powerful tool exploiting future research, including genetics genomics.

Language: Английский

Citations

21