Plant Communications, Journal Year: 2024, Volume and Issue: 5(10), P. 101046 - 101046
Published: Aug. 8, 2024
This paper introduces CentIER, the first bioinformatic tool designed to detect complete centromeric regions without additional wet experiments. The accuracy of CentIER was validated on diverse plant genomes such as Arabidopsis, rice, maize and mulberry, results show that can perform significantly more accurate detection than existing tool.
Language: Английский
Molecular Plant, Journal Year: 2023, Volume and Issue: 16(11), P. 1733 - 1742
Published: Sept. 22, 2023
Language: Английский
Citations
1284
Horticulture Research, Journal Year: 2023, Volume and Issue: 10(8)
Published: June 13, 2023
A high-quality genome is the basis for studies on functional, evolutionary, and comparative genomics. The majority of attention has been paid to solution complex chromosome structures highly repetitive sequences, along with emergence a new 'telomere-to-telomere (T2T) assembly' era. However, bioinformatic tools automatic construction and/or characterization T2T are limited. Here, we developed user-friendly web toolkit, quarTeT, which currently includes four modules: AssemblyMapper, GapFiller, TeloExplorer, CentroMiner. First, AssemblyMapper designed assemble phased contigs into chromosome-level by referring closely related genome. Then, GapFiller would endeavor fill all unclosed gaps in given aid additional ultra-long sequences. Finally, TeloExplorer CentroMiner applied identify candidate telomere centromere as well their localizations each chromosome. These modules can be used alone or combination other assembly characterization. As case study, adopting entire modular functions have achieved
Language: Английский
Citations
109
Genome Research, Journal Year: 2024, Volume and Issue: 34(2), P. 161 - 178
Published: Feb. 1, 2024
Centromeres are essential regions of eukaryotic chromosomes responsible for the formation kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, underlying DNA sequences diverse both within and between species predominantly repetitive nature. The repeat content includes high-copy tandem repeats (satellites), and/or specific families transposons. functional region centromere is defined by loading histone 3 variant (CENH3), nucleates shows dynamic regulation. In many plants, composed satellite arrays that densely methylated invaded centrophilic retrotransposons. some cases, retrotransposons become sites CENH3 loading. We review structure plant centromeres, including monocentric, holocentric, metapolycentric architectures, vary number distribution attachment along chromosomes. discuss how variation can drive genome elimination early divisions embryogenesis. epigenetic state may influence identity evolutionary models seek explain paradoxically rapid change observed across species, potential roles recombination. outline putative modes selection could act as well role driving cycles evolution. Although our primary focus on genomes, we draw comparisons with animal fungal derive eukaryote-wide perspective function.
Language: Английский
Citations
30
PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(2), P. 1401 - 1413
Published: Jan. 29, 2024
Abstract Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors artificially selected for desired agronomic traits along with dramatic genomic variation in course of moderate to severe bottlenecks. However, previous investigations mainly focused on small-effect variants, while changes gene contents rarely investigated due lack population-level assemblies both and its relatives. Here, we applied comparative analyses discover gain loss grapevine using long-read representative population samples domesticated grapevines (V. vinifera ssp. vinifera) their sylvestris). Only ∼7% families were shared 16 Vitis genomes ∼8% specific each accession, suggesting variations genomes. Compared progenitors, accessions exhibited an increased presence genes associated asexual reproduction, showcased a higher abundance related pollination, revealing transition from sexual reproduction clonal propagation processes. Moreover, harbored fewer disease-resistance than progenitors. The SVs occurred frequently aroma between indicating rapid diversification these domestication. Our study provides insights resources biological studies breeding programs grapevine.
Language: Английский
Citations
17
Horticulture Research, Journal Year: 2023, Volume and Issue: 10(9)
Published: Aug. 1, 2023
Abstract Banana is one of the most important crops world. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half global banana production, thereby are great significance human societies. However, until now, high-quality haplotype-resolved reference genome was still undecoded cultivars. Here, we reported telomere-to-telomere (T2T) and ‘Baxijiao’ (Cavendish) consisting three haploid assemblies. The sizes assemblies were estimated to be 477.16 Mb, 477.18 469.57 respectively. Although with origins, showed differences low levels sequence collinearity. Several large reciprocal translocations identified among chromosomes 1, 4, 7. An expansion gene families that might affect fruit quality aroma detected, such as those belonging sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch aromatic compound biosynthetic process. Besides, an related anther pollen development observed, could associated parthenocarpy sterility Cavendish cultivar. Finally, much fewer resistance genes in than M. acuminata, particularly clusters 3 10, providing potential targets explore molecular analysis disease banana. This T2T will thus valuable genetic resource biological studies, breeding, improvement
Language: Английский
Citations
32
Horticulture Research, Journal Year: 2023, Volume and Issue: 10(7)
Published: May 31, 2023
Abstract Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health environment cannot be overstated. However, mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report assembly analysis telomere-to-telomere gap-free genome species, Morus notabilis, which has emerged as an important in gene function research genetic improvement. The produced here provides unprecedented opportunity for us to study structure centromeres. Our results revealed that all centromeric regions share conserved satellite repeats with different copies. Strikingly, found M. notabilis species polycentric chromosomes only chromosome up now. We propose compelling model explains formation mechanism new centromeres addresses unsolved scientific question fusion-fission cycle species. sheds light functional genomics, evolution, improvement
Language: Английский
Citations
24
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
13
Horticulture Research, Journal Year: 2024, Volume and Issue: 11(3)
Published: Jan. 17, 2024
Abstract Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, gap-free assembly with genome size of 414.3 Mb 31,251 coding genes was obtained for suaveolens ‘Variegata’. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, sizes 401.9 405.7 Mb, respectively. The telomeres centromeres each haplotype almost fully annotated. addition, we detected total 41,135 structural variations. Enrichment analysis demonstrated that involved in terpenoid biosynthesis affected these Analysis volatile metabolites showed M. mainly produces piperitenone oxide rather than We identified three the encode isopiperitenone reductase (ISPR), key rate-limiting enzyme menthol biosynthesis. However, transcription levels ISPR low. Given other expressed, ISPRs may account accumulation species. findings study provide valuable resource improving detection rate accuracy genetic variants, thereby enhancing our understanding their impact gene function expression. Moreover, haplotype-resolved offers novel insights into molecular marker-assisted breeding Mentha.
Language: Английский
Citations
12
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
Plant Stress, Journal Year: 2024, Volume and Issue: 11, P. 100356 - 100356
Published: Jan. 21, 2024
Crop resilience measures must be strengthened in response to the global climate impact. Temperature stress exacerbates impact on crop growth and grain yield, threatening sustainability of grapevine production dependent wine industries. Grape (Vitis spp.) is one most widely cultivated fruit crops world, as well economically important fruit. However, grape yield quality are highly environmental conditions, particularly temperature stress. Understanding molecular mechanisms that control responses stresses development stress-resilient varieties have markedly advanced through rapid evolution high-throughput sequencing technologies, state-of-the-art multi-omics analytic platforms, automated phenotyping facilities. In current review, we summarized recent genomic progress omics-based breakthroughs grapes contributed abiotic tolerance via genetic strategies during last decades. Furthermore, delve into prospective challenges opportunities pertaining use multi-omics-based breeding aimed at designing climate-resilient varieties. Advances efficient de novo or re-domestication histories, characterization numerous trait genes using various omics tools, also discussed. By describing underlying adaptability future meet demand due population bursts following decades while keeping change mind, information will offer potential solutions for sustainable businesses.
Language: Английский
Citations
10