A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (Ribes nigrum L.) DOI Creative Commons

Freya Maria Rosemarie Ziegler,

Victoria Cozer Rosenthal, José G. Vallarino

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 12(2)

Published: Nov. 11, 2024

Abstract Blackcurrant (Ribes nigrum L., family Grossulariaceae) is a perennial shrub that widely cultivated for its edible berries. These are rich in antioxidants, vitamin C, and anthocyanins, making them valuable ingredient the food beverage industry. However, prolonged periods of drought during fruiting season lead to stress, which has serious ecological agricultural implications, inhibiting blackcurrant growth reducing yields. To facilitate analysis underlying molecular processes, we present first high-quality chromosome-scale partially haplotype-resolved assembly genome (cv. Rosenthals Langtraubige), also Grossulariaceae. We used this genomic reference analyze transcriptomic response leaves roots revealing differentially expressed genes with diverse functions, including those encoding transcription factors bZIP, bHLH, MYB, WRKY, tyrosine kinase-like kinases such as PERK DUF26. Gene expression was correlated abundance primary metabolites, 14 significant differences between stressed controls indicating metabolic stress. Amino acids proline were more abundant under stress conditions, whereas organic depleted. The data from study can be develop robust cultivars thrive conditions.

Language: Английский

Genomic analysis reveals phylogeny of Zygophyllales and mechanism for water retention of a succulent xerophyte DOI
Qing Ma, Hai-Shuang Liu, Hu-Jun Li

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(1), P. 617 - 639

Published: Jan. 29, 2024

Abstract Revealing the genetic basis for stress-resistant traits in extremophile plants will yield important information crop improvement. Zygophyllum xanthoxylum, an extant species of ancient Mediterranean, is a succulent xerophyte that can maintain favorable water status under desert habitats; however, this adaptive trait poorly understood. Furthermore, phylogenetic position Zygophyllales, to which Z. xanthoxylum belongs, remains controversial. In study, we sequenced and assembled chromosome-level genome xanthoxylum. Phylogenetic analysis showed Zygophyllales Myrtales form separated taxon as sister clade comprising fabids malvids, clarifying at whole-genome scale. Analysis genomic transcriptomic data revealed multiple critical mechanisms underlying efficient osmotic adjustment using Na+ K+ “cheap" osmolytes has evolved through expansion synchronized expression genes encoding key transporters/channels their regulators involved Na+/K+ uptake, transport, compartmentation. It worth noting ZxCNGC1;1 (cyclic nucleotide-gated channels) ZxCNGC1;2 constituted previously undiscovered energy-saving pathway uptake. Meanwhile, core biosynthesis cuticular wax also featured upregulated expression, contributing retention capacity environments. Overall, these findings boost understanding evolutionary relationships eudicots, illustrate unique mechanism distinct from glycophyte, thus provide valuable resources improvement stress tolerance crops insights into remediation sodic lands.

Language: Английский

Citations

6
Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes DOI
Meizhen Wang, Mengmeng Zhu, Jiayi Qian

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 197, P. 108093 - 108093

Published: May 11, 2024

Language: Английский

Citations

5
Long repeat sequences mediated multiple mitogenome conformations of mulberries (<i>Morus</i> spp.), an important economic plant in China DOI
Luxian Liu, Long Qian,

Weiwei Lv

et al.

Published: Jan. 1, 2024

Language: Английский

Citations

4
SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics DOI Creative Commons
Rengang Zhang,

Hong-Yun Shang,

Richard I. Milne

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: April 10, 2025

Abstract With the explosive growth of whole-genome datasets, accurate detection orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods identifying face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable robust approach, based on Orthology Index (OI), to effectively identify Our evaluation across large-scale empirical dataset diverse polyploidization events demonstrated high reliability robustness OI method. Simulation-based benchmarks further validated accuracy our method, showing its superior performance against existing wide range scenarios. Additionally, explored broad applications plant genomes, including inference polyploidy, identification reticulation, phylogenomics. conclusion, offers robust, interpretable, approach synteny, facilitating more efficient analyses genomics.

Language: Английский

Citations

0
Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales DOI Creative Commons
Lin‐Bo Jia, Shuying Wang, Jinjin Hu

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: April 12, 2024

Abstract Background The “woody clade” in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node the angiosperm tree of life, as interfamilial relationships WCS remain contentious. Based on comprehensive sampling genera, this study aims to recover robust maternal backbone phylogeny by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), parsimony (MP) methods, explore possible causes phylogenetic recalcitrance with respect deep within WCS, combination molecular fossil evidence. Results Although were identically resolved monophyletic, MP analysis recovered different topologies for among Altingiaceae, Daphniphyllaceae from ML BI phylogenies. fossil-calibrated plastome showed that underwent rapid divergence crown groups early Cretaceous (between 104.79 100.23 Ma), leading origin stem lineage ancestors Hamamelidaceae very short time span (∼4.56 Ma). Compared topology previous based nuclear data, cytonuclear discordance regarding was detected. Conclusions Molecular evidence imply might have experienced radiative diversification groups, extensive extinctions at genus species levels around Cretaceous/Paleocene boundary, ancient hybridization. Such evolutionarily complex events may introduce biases topological estimations due incomplete sorting, discordance, long-branch attraction, potentially impacting accurate reconstruction relationships.

Language: Английский

Citations

3
Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL DOI Creative Commons
Hong‐Yun Shang, Kai‐Hua Jia, Minjie Zhou

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 3, 2024

Abstract Incomplete lineage sorting (ILS) and introgression/hybridization (IH) is prevalent in nature thus frequently result discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability numerous tools for detecting ILS IH among species, many these are lacking effective visualization, or time-consuming, require prior predetermination. Here, we addressed shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining indices quantify IH, this can detect extent lineages with high reliability, visualize them based on gene topology patterns constructed using ASTRAL. We tested Phytop extensively both simulated real data, found that it enables users quickly conveniently estimate clarifying uncertainty. available at https://github.com/zhangrengang/phytop expected contribute intuitive inference genetic relationships future research.

Language: Английский

Citations

2
Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL DOI Creative Commons

Hong-Yun Shang,

Kai‐Hua Jia,

Naiwei Li

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 21, 2024

Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature thus frequently result discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability numerous tools for detecting ILS IH among species, many these lack effective visualization, or time-consuming, require prior predetermination. Here, we addressed shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining indices quantify IH, this can detect extent lineages with high reliability, visualize them based on gene topology patterns constructed using ASTRAL. We tested Phytop extensively both simulated real data, found that it enables users quickly conveniently estimate clarifying uncertainty. is available at https://github.com/zhangrengang/phytop expected contribute intuitive convenient inference genetic relationships future research.

Language: Английский

Citations

2
Insights into the Superrosids phylogeny and flavonoid synthesis from the telomere-to-telomere gap-free genome assembly of Penthorum chinense Pursh DOI Creative Commons

Zhoutao Wang,

Junmei Zhou, Junjie Pan

et al.

Horticulture Research, Journal Year: 2023, Volume and Issue: 11(2)

Published: Dec. 19, 2023

The completion of the first telomere-to-telomere (T2T) genome assembly

Language: Английский

Citations

5
Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes DOI Creative Commons
Rengang Zhang,

Hong-Yun Shang,

Richard I. Milne

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 23, 2024

Abstract With the explosive growth of whole-genome datasets, accurate detection orthologous synteny has become crucial for reconstruction evolutionary history. However, currently available methods identification have great limitations: are difficult to scale with varying polyploidy histories, and removal out-paralogy is challenging. In this study, we developed a scalable robust approach, Orthology Index ( OI ), identify synteny. Our evaluation large-scale dataset diverse polyploidization events demonstrated that technique highly reliable. This discovery highlights as potentially unified criterion synteny, further validated using simulation-based benchmarks. addition, explore its broad applications in reconstructing histories plant genomes, including inference polyploidy, reticulation, phylogenomics. conclusion, offers robust, interpretable, approach identifying significantly enhancing our analytical prowess genomics.

Language: Английский

Citations

1
Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes DOI Creative Commons
Kai‐Hua Jia, Rengang Zhang,

Hong-Yun Shang

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 23, 2024

Abstract We developed a scalable and robust approach, the Orthology Index (OI), to accurately identify orthologous synteny by calculating proportion of pre-inferred orthologs within syntenic blocks. Our evaluation comprehensive dataset comprising nearly 100 known cases with diverse polyploidy events revealed that approach is highly reliable in identification synteny. This discovery highlights OI as potentially universal criterion for automated Additionally, we demonstrate its broad applications reconstructing plant genome evolutionary histories, including reticulation inference, phylogenomics. The index packaged an all-in-one toolkit (https://github.com/zhangrengang/OrthoIndex).

Language: Английский

Citations

1