The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(3), P. 641 - 652

Published: Dec. 17, 2020

Abstract The quality of genome assemblies has improved rapidly in recent years due to continual advances sequencing technology, assembly approaches, and control. In the field molecular ecology, this led development exceptional that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, population genomics naturally occurring species. Moreover, extent which a single reference represents diversity within species varies: pan‐genomes become increasingly ecological resources, particularly systems found have considerable presence‐absence variation their functional content. Here, we highlight technology raised bar provide guidance on standards achieve genomes. Key recommendations include following: (a) Genome should long‐read except rare cases where it is effectively impossible acquire adequately preserved samples needed high weight DNA standards. (b) At least one scaffolding approach included with such as Hi‐C or optical mapping. (c) carefully evaluated, may involve utilising short read data polishing, error correction, k‐mer analyses, estimating percent reads map back an assembly. Finally, most valuable if all methods are made publicly available utility further verified through examples. While these based current anticipate future push ecology community continue adopt new approaches attain highest assemblies.

Language: Английский

---

The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine

The Plant Journal, Journal Year: 2020, Volume and Issue: 105(6), P. 1495 - 1506

Published: Dec. 10, 2020

Vitis amurensis (Shanputao) is the most cold tolerant species and so of great interest to grape breeders producers in areas with low winter temperatures. Here, we report its high-quality, chromosome-level genome assembly based on a combination sequence data from Illumina PacBio platforms, BioNano optical mapping high-throughput chromosome conformation Capture (Hi-C) mapping. The 604.56-Mb contains 32 885 protein-coding genes. Shanputao was found share common ancestor PN40024 (V. vinifera) approximately 2.17-2.91 million years ago, gene expansion observed might contribute enhancement tolerance. Transcriptome analysis revealed 17 genes involved signal transduction, suggesting that there different response mechanism chilling temperature freezing conditions. Furthermore, genome-wide association study uncovered phosphoglycerate kinase may resistance buds winter. not only represents valuable resource for breeders, but also important clarifying molecular mechanisms

Language: Английский

---

Unraveling a genetic roadmap for improved taste in the domesticated apple

Molecular Plant, Journal Year: 2021, Volume and Issue: 14(9), P. 1454 - 1471

Published: May 19, 2021

Language: Английский

---

Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: March 4, 2021

Tartaric acid (TA) is an obscure end point to the catabolism of ascorbic (Asc). Here, it proposed as a “specialized primary metabolite”, originating from carbohydrate metabolism but with restricted distribution within plant kingdom and lack known function in metabolic pathways. Grapes fall into list high TA-accumulators, biosynthesis occurring both leaf berry. Very little TA biosynthetic pathway enzymes any species, although recently some progress has been made this space. New technologies grapevine research such development global co-expression network analysis tools genome-wide association studies, should enable more rapid progress. There also information regarding roles for organic metabolism. Therefore review aims briefly summarize current knowledge about key intermediates grapes regulation its precursor, ascorbate, followed by speculative discussion around potential based on Asc metabolism, other aspects fruit

Language: Английский

---

The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Dec. 21, 2021

Abstract In order to elucidate the still controversial processes that originated European wine grapes from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show all analyses support a single domestication event occurred in Western Asia was followed by numerous pervasive introgressions populations. This admixture generated so-called international have diffused Alpine countries worldwide. Across Europe, marked differences genomic diversity are observed local varieties traditionally cultivated different producing countries, with Italy France showing largest diversity. Three regions reduced genetic observed, presumably as consequence artificial selection. lowest region, two candidate genes gained berry–specific expression domesticated may contribute change berry size morphology makes fruit attractive for human consumption adapted winemaking.

Language: Английский

---

Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits

Theoretical and Applied Genetics, Journal Year: 2021, Volume and Issue: 134(6), P. 1829 - 1843

Published: May 20, 2021

Abstract Key message Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery climate-resilient nutrient rich crops for future food security. Accelerating genetic gain in crop improvement programs with respect climate resilience nutrition traits, realization improved farmers’ fields require integration several approaches. This article focuses on innovative approaches address components equation. A prerequisite enhancing variance ( σ 2 g ) is identification or creation favorable alleles/haplotypes their deployment improving key traits. Novel alleles new existing target traits need be accessed added population while maintaining diversity. Selection intensity i program can by testing a larger size, enabled statistical designs minimal replications high-throughput phenotyping. priorities criteria select appropriate portion too assume an important role. The most component breeder′s heritability h ). Heritability estimates depend factors including size type methods. present starts brief discussion potential ways enhance population. We highlight experimental that improve trait estimation. also offer perspective reducing cycle time t ), which achieved through selection parents, optimizing scheme, rapid fixation alleles, combining speed optimize trials release. Finally, we summarize knowledge from multiple disciplines gains nutritional

Language: Английский

---

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

Quantitative Plant Biology, Journal Year: 2022, Volume and Issue: 3

Published: Jan. 1, 2022

Abstract Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing technologies enable scientists to investigate even large complex genomes. Sequencing projects can be conducted by single research groups sequences of smaller genomes completed within days. This also resulted in an increased investigation from multiple species scale address fundamental questions associated with the origin evolution land plants. Increased accessibility devices user-friendly software allows more researchers get involved Current challenges accurately resolving diploid or polyploid genome better accounting for intra-specific diversity switching use reference a pangenome graph.

Language: Английский

---

Plant genome resequencing and population genomics: Current status and future prospects

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(8), P. 1252 - 1268

Published: July 27, 2023

Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity plants to exploring their functional significance delivering beneficial alleles for improvement. This transformation been facilitated by increasing adoption of whole-genome resequencing. In this review, we summarize current progress population-based genome resequencing studies how these affect A total 187 land 163 countries resequenced, comprising 54 413 accessions. As part efforts 367 traits surveyed 86 genome-wide association conducted. Economically important crops, particularly cereals, vegetables, legumes, dominated efforts, leaving gap 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing global perspective on genomics. We highlight genes that selected during domestication, or associated with agronomic traits, form repository candidate future research application. Despite opportunities cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. call more open collaborative approach promotes data sharing encourages contribution-based credit policy. number will continue rise decreasing costs, coupled advances analysis computational technologies. expansion, terms both scale quality, holds promise deeper insights into trait breeding design.

Language: Английский

---

On the concepts and measures of diversity in the genomics era

Current Plant Biology, Journal Year: 2023, Volume and Issue: 33, P. 100278 - 100278

Published: Jan. 1, 2023

Diversity serves as the foundation for breeding and evolution. In science of genomics, investigation genetic variation has long been a prominent subject. Researchers now have access to previously unheard volumes data, thanks development new genomic technologies which allow them thoroughly examine complexity variation. As result, definitions measurements diversity created, taking into consideration things like how is distributed throughout populations, impact natural selection, connection between phenotypic diversity. One crucial idea "genetic ancestry" describes percentage person's composition that may be linked particular ancestral populations. Heterozygosity, measures degree within population, another indicator Recent developments in genomics resulted creation tools methodologies examining addition these conventional measurements. Generally, area research rapidly changing age, with theories being created on regular basis. The origins effects are expected continue revealed our knowledge deepens, substantial ramifications human health, evolutionary biology, variety other domains.

Language: Английский

---

Advances in understanding cold tolerance in grapevine

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 192(3), P. 1733 - 1746

Published: Feb. 15, 2023

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes buds of grapevine should withstand low temperatures (LTs) annually during winter. However, widely cultivated Vitis vinifera cold-sensitive cannot survive severe winter in regions with extremely LTs, such as viticulture northern China. By contrast, few wild species like V. amurensis riparia exhibit excellent freezing tolerance. mechanisms underlying cold tolerance remain largely unknown. In recent years, much progress has been made elucidating mechanisms, owing to advances sequencing molecular biotechnology. Assembly genomes together resequencing transcriptome data enable researchers conduct genomic transcriptomic analyses various genotypes populations explore genetic variations involved addition, number pivotal genes have identified functionally characterized. this review, we summarize major physiological put forward questions field. We also discuss strategies for improving stress. Understanding will facilitate development grapevines adaption global climate change.

Language: Английский

---