Genome assembly in the telomere-to-telomere era

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(9), P. 658 - 670

Published: April 22, 2024

Language: Английский

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Plant pangenomes for crop improvement, biodiversity and evolution

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

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Genomic language models: opportunities and challenges

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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The genome awakens: transposon-mediated gene regulation

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(3), P. e1011174 - e1011174

Published: March 4, 2024

A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis -regulatory sequences. It remains unclear how such drastic evolution across species allows preservation of gene function, to what extent these differences influence cis- regulatory variation arising within impacts phenotypic change. Here, we investigated questions using a plant stem cell regulator in ~125 million years. Using in-vivo genome editing two distantly related models, Arabidopsis thaliana (Arabidopsis) Solanum lycopersicum (tomato), generated 70 deletion alleles the upstream downstream regions repressor CLAVATA3 ( CLV3 ) compared their individual combined effects on shared phenotype, number carpels make fruits. We found sequences tomato are highly sensitive even small perturbations its region. In contrast, tolerant severe disruptions both coding sequence. Combining deletions also revealed different outcome. Whereas enhancement from adding mutations was predominantly weak additive tomato, mutating caused substantial synergistic effects, demonstrating distinct distribution redundancy functional Our results demonstrate remarkable malleability structural organization deeply suggest major reconfiguration sequence space common yet cryptic evolutionary force altering genotype-to-phenotype relationships genes. Finally, our findings underscore need for lineage-specific dissection spatial architecture -regulation effectively engineer trait productivity crops.

Language: Английский

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Cross-species plant genomes modeling at single nucleotide resolution using a pre-trained DNA language model

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

Published: June 5, 2024

Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pre-trained on large-scale biological sequences can learn evolutionary conservation offer cross-species prediction better than supervised through fine-tuning limited labeled data. We introduce PlantCaduceus, a DNA LM based the Caduceus Mamba architectures, curated dataset of 16 Angiosperm genomes. Fine-tuning PlantCaduceus Arabidopsis data for four tasks, including predicting translation initiation/termination sites splice donor acceptor sites, demonstrated high transferability to 160 million year diverged maize, outperforming best existing by 1.45 7.23-fold. is competitive state-of-the-art protein LMs terms deleterious mutation identification, threefold PhyloP. Additionally, successfully identifies well-known causal variants both maize. Overall, versatile that accelerate genomics crop breeding applications.

Language: Английский

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Towards an unbiased characterization of genetic polymorphism

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

Published: May 30, 2024

Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to nearly complete genome sequences for population samples, should solve the problem—except characterizing making sense non-SNP variation difficult even with perfect sequence data. Here, we analyze 27 genomes Arabidopsis thaliana in an attempt address these issues, illustrate what can be learned analyzing whole-genome data unbiased manner. Estimated sizes range from 135 155 Mb, differences almost entirely due centromeric rDNA repeats. The completely assembled chromosome arms comprise roughly 120 Mb all accessions, but full structural variants, many caused insertions transposable elements (TEs) subsequent partial deletions such insertions. Even only pan-genome coordinate system includes resulting ends up being 40% larger than size any one genome. analysis reveals incompletely annotated mobile-ome: our ability predict actually moving poor, detect several novel TE families. In contrast this, genic portion, or “gene-ome”, highly conserved. By annotating each using accession-specific transcriptome data, find 13% genes segregating most transcriptionally silenced. Finally, show short-read previously massively underestimated kinds, including SNPs—mostly regions where short reads could not mapped reliably, also were incorrectly. We demonstrate SNP-calling errors biased choice reference genome, RNA-seq BS-seq results strongly affected mapping rather assayed individual. conclusion, while pose tremendous analytical challenges, they will ultimately revolutionize understanding evolution.

Language: Английский

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Demand-side and supply-side factors for accelerating varietal turnover in smallholder soybean farms

Journal of Cleaner Production, Journal Year: 2024, Volume and Issue: 447, P. 141372 - 141372

Published: Feb. 20, 2024

The rapid growth of soybean cultivation in the world augurs well for achieving SDG2 promoting sustainable agriculture, ending hunger, food security, and improving nutrition. India started 1970s to combat dietary protein deficiencies augment smallholders' incomes. However, yield remains low plateaued at one ton per hectare past three decades. This paper leverages a large primary dataset explores speed varietal change by applying survival functions analyzing determinants turnover time employing dynamic framework harnessing duration analysis. results show that adopting leading varieties has reached saturation policy intervention can have an immediate impact. weighted average age farmers' fields is relatively high 16 years, implying slower rate. lack improved with desirable traits, poor information flow, growers' preference traits beyond yield-hamper faster substitution. Further, analysis indicates regional variations driving replacement. findings significant implications spurring yields through investments development, leveraging modern molecular methods long juvenility photo-insensitivity, disseminating information, institutional changes enabling private sector participation crop breeding.

Language: Английский

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Taxonomic and molecular characterization of 15 wild-growing tulip species of Greece using the internal transcribed spacer (ITS) nuclear marker in combination with the psb A- trn H and trn L/ trn F plastid markers

Biotechnology & Biotechnological Equipment, Journal Year: 2024, Volume and Issue: 38(1)

Published: April 1, 2024

Due to the absence or scarcity of DNA sequence data in GenBank regarding Mediterranean, Balkan Greek native tulip species, we performed molecular characterization 15 wild-growing species through analysis internal transcribed spacer nrDNA and psbA/trnH trnL/trnF cpDNA regions. To facilitate conservation sustainable utilization efforts, aim was identify complement genetic distinctiveness six endemic five Aegean and/or subendemic tulips two naturalized ones Asiatic origin, among which seven are threatened with extinction. Molecular phylogenetic 148 sequences conducted, 85 Tulipa taxa (species subspecies) were aligned compared 40 new generated herein for tulips. These three markers resulted 354 single-nucleotide polymorphisms (SNPs) 20 distinct indels all taxa, 100 SNPs 12 related Phylogenetic dendrograms constructed above-mentioned markers, analyzed separately jointly, leading clusters Group 1 included members subgenus Tulipa, that is, T. scardica, undulatifolia, rhodopea, agenensis raddii; 2 only clusiana (subgenus Clusianae) 3 Eriostemones, *T. bakeri, saxatilis, australis, cretica, goulimyi, orphanidea bithynica, hageri doerfleri (asterisks indicate single-country endemics).

Language: Английский

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Whole-Genome Alignment: Methods, Challenges, and Future Directions

Applied Sciences, Journal Year: 2024, Volume and Issue: 14(11), P. 4837 - 4837

Published: June 3, 2024

Whole-genome alignment (WGA) is a critical process in comparative genomics, facilitating the detection of genetic variants and aiding our understanding evolution. This paper offers detailed overview categorization WGA techniques, encompassing suffix tree-based, hash-based, anchor-based, graph-based methods. It elaborates on algorithmic properties these tools, focusing performance methodological aspects. underscores latest progress WGA, emphasizing increasing capacity to manage growing intricacy volume genomic data. However, field still grapples with computational biological hurdles affecting precision speed WGA. We explore challenges potential future solutions. aims provide comprehensive resource for researchers, deepening tools their applications, constraints, prospects.

Language: Английский

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