The structure, function, and evolution of plant centromeres DOI Creative Commons
Matthew Naish, Ian R. Henderson

Genome Research, Год журнала: 2024, Номер 34(2), С. 161 - 178

Опубликована: Фев. 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.

Язык: 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

и другие.

Molecular Plant, Год журнала: 2023, Номер 16(11), С. 1733 - 1742

Опубликована: Сен. 22, 2023

Язык: Английский

Процитировано

1429
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing DOI Creative Commons
Michael Alonge,

Ludivine Lebeigle,

Melanie Kirsche

и другие.

Genome biology, Год журнала: 2022, Номер 23(1)

Опубликована: Дек. 15, 2022

Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, establish chromosome-scale reference genomes the widely used tomato genotype M82 along with Sweet-100, new rapid-cycling that developed to accelerate functional editing in tomato. This work outlines strategies rapidly expand genomic resources other plant species.

Язык: Английский

Процитировано

486
Complete genomic and epigenetic maps of human centromeres DOI
Nicolas Altemose, Glennis A. Logsdon, Andrey V. Bzikadze

и другие.

Science, Год журнала: 2022, Номер 376(6588)

Опубликована: Март 31, 2022

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric centromeric repeats, constitute 6.2% the (189.9 megabases). Detailed maps these regions revealed multimegabase structural rearrangements, including in active repeat arrays. Analysis centromere-associated uncovered strong relationship between position centromere evolution surrounding DNA through layered expansions. Furthermore, comparisons X centromeres across diverse panel individuals illuminated high degrees structural, epigenetic, sequence variation complex rapidly evolving regions.

Язык: Английский

Процитировано

387
A complete telomere-to-telomere assembly of the maize genome DOI Creative Commons
Jian Chen,

Zijian Wang,

Kaiwen Tan

и другие.

Nature Genetics, Год журнала: 2023, Номер 55(7), С. 1221 - 1231

Опубликована: Июнь 15, 2023

Abstract A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a assembly maize with each chromosome entirely traversed in single contig. The 2,178.6 Mb T2T Mo17 base accuracy over 99.99% unveiled structural features all repetitive regions genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine–adenine–guanine (TAG) tri-nucleotide repeats up to 235 kb. entire nucleolar organizer region 26.8 array 2,974 45S rDNA copies revealed enormously complex patterns duplications transposon insertions. Additionally, assemblies ten centromeres enabled us precisely dissect repeat compositions both CentC-rich CentC-poor centromeres. represents major step forward understanding complexity highly recalcitrant higher plant genomes.

Язык: Английский

Процитировано

162
High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads DOI Creative Commons
Bo Wang, Xiaofei Yang, Yanyan Jia

и другие.

Genomics Proteomics & Bioinformatics, Год журнала: 2021, Номер 20(1), С. 4 - 13

Опубликована: Сен. 3, 2021

Abstract Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, genomics. However, the latest version of reference genome still contains a significant number missing segments. Here, we reported high-quality almost complete Col-0 assembly with two gaps (named Col-XJTU) by combining Oxford Nanopore Technologies ultra-long reads, Pacific Biosciences high-fidelity long Hi-C data. The total size 133,725,193 bp, introducing 14.6 Mb novel sequences compared to TAIR10.1 genome. All five chromosomes Col-XJTU are highly accurate consensus quality (QV) scores > 60 (ranging from 62 68), which higher than those 45 52). We completely resolved chromosome (Chr) 3 Chr5 in telomere-to-telomere manner. Chr4 was except nucleolar organizing regions, comprise repetitive DNA fragments. Chr1 centromere (CEN1), reportedly around 9 length, particularly challenging assemble due presence tens thousands CEN180 satellite repeats. Using cutting-edge sequencing data computational approaches, assembled 3.8-Mb-long CEN1 3.5-Mb-long CEN2. also investigated structure epigenetics centromeres. Four clusters monomers were detected, centromere-specific histone H3-like protein (CENH3) exhibited strong preference Cluster 3. Moreover, observed hypomethylation patterns CENH3-enriched regions. believe that this assembly, Col-XJTU, would serve as valuable better understand global pattern centromeric polymorphisms, well genetic epigenetic features plants.

Язык: Английский

Процитировано

135
A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding DOI Creative Commons
Yun Deng, Shoucheng Liu, Yilin Zhang

и другие.

Molecular Plant, Год журнала: 2022, Номер 15(8), С. 1268 - 1284

Опубликована: Июнь 23, 2022

Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with gaps and a narrow genetic base hinder functional genomics improvement of watermelon. Here, we report assembly telomere-to-telomere gap-free genome elite watermelon inbred line G42 by incorporating high-coverage accurate long-read sequencing data multiple strategies. All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps, representing highest completeness quality to date. The reference 369 321 829 bp in length contains 24 205 predicted protein-coding genes, all 22 telomeres centromeres characterized. Furthermore, established pollen-EMS mutagenesis protocol obtained over 200 000 M1 seeds from . In sampling pool, 48 monogenic phenotypic mutations, selected 223 78 M2 mutants morphological changes, were confirmed. average mutation density was 1 SNP/1.69 Mb indel/4.55 per plant SNP/1.08 indel/6.25 plant. Taking advantage genome, 8039 mutations 32 plants sampled families identified 100% accuracy, whereas only 25% randomly using 97103v2 could be Using this library two genes responsible for elongated shape male sterility (ClMS1) identified, both caused single change G A. validated its EMS provide invaluable resources

Язык: Английский

Процитировано

129
The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding DOI Creative Commons

Xiaoya Shi,

Shuo Cao, Xu Wang

и другие.

Horticulture Research, Год журнала: 2023, Номер 10(5)

Опубликована: Апрель 4, 2023

Grapevine is one of the most economically important crops worldwide. However, previous versions grapevine reference genome tipically consist thousands fragments with missing centromeres and telomeres, limiting accessibility repetitive sequences, centromeric telomeric regions, study inheritance agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free for cultivar PN40024 using PacBio HiFi long reads. The T2T (PN_T2T) 69 Mb longer 9018 more genes identified than 12X.v0 version. We annotated 67% 19 36 incorporated gene annotations into PN_T2T assembly. detected total 377 clusters, which showed associations complex traits, such as aroma disease resistance. Even though derives from nine generations selfing, still found genomic hotspots heterozygous sites associated biological processes, oxidation-reduction process protein phosphorylation. fully complete therefore constitutes an resource genetic studies breeding programs.

Язык: Английский

Процитировано

124
quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification DOI Creative Commons
Yunzhi Lin, Chen Ye,

Xingzhu Li

и другие.

Horticulture Research, Год журнала: 2023, Номер 10(8)

Опубликована: Июнь 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

Язык: Английский

Процитировано

124
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps DOI Open Access
Mitchell R. Vollger, Peter Kerpedjiev, Adam M. Phillippy

и другие.

Bioinformatics, Год журнала: 2022, Номер 38(7), С. 2049 - 2051

Опубликована: Янв. 7, 2022

Abstract Summary The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence telomere-to-telomere assemblies with multi-megabase requires new strategies. Here, we introduce StainedGlass, which can generate publication-quality figures interactive visualizations that depict identity orientation tandem repeat structures at a genome-wide scale. tool rapidly reveal higher-order improve inference evolutionary history for some most complex regions genomes. Availability implementation StainedGlass implemented Snakemake available open source under MIT license https://mrvollger.github.io/StainedGlass/. Supplementary information data are Bioinformatics online.

Язык: Английский

Процитировано

105
Evolutionary analysis of a complete chicken genome DOI Creative Commons
Zhen Huang,

Zaoxu Xu,

Hao Bai

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(8)

Опубликована: Фев. 13, 2023

Microchromosomes are prevalent in nonmammalian vertebrates [P. D. Waters et al. , Proc. Natl. Acad. Sci. U.S.A. 118 (2021)], but a few of them missing bird genome assemblies. Here, we present new chicken reference containing all autosomes, Z and W chromosome, with gaps closed except for the W. We identified ten small microchromosomes (termed dot chromosomes) distinct sequence epigenetic features, among which six were newly assembled. Those chromosomes exhibit extremely high GC content level DNA methylation enriched housekeeping genes. The pericentromeric heterochromatin is disproportionately large continues to expand proliferation satellite testis-expressed Our analyses revealed that 41-bp CNM repeat frequently forms higher-order repeats (HORs) at centromeres acrocentric chromosomes. centromere core regions where kinetochore attaches often encompass telomeric (TTAGGG)n, one chromosomes, recruits an endogenous retrovirus (ERV). further demonstrate chromosome shares some common features having arrays hypermethylated tandem repeats. Finally, using complete models, reconstructed fine picture chordate karyotype evolution, revealing frequent chromosomal fusions before after vertebrate whole-genome duplications. characterization shed insights into understanding evolution biology.

Язык: Английский

Процитировано

95