Haplotype‐resolved genome assembly of Populus tremula × P. alba reveals aspen‐specific megabase satellite DNA DOI Creative Commons
Ran Zhou, Jerry Jenkins, Yibing Zeng

и другие.

The Plant Journal, Год журнала: 2023, Номер 116(4), С. 1003 - 1017

Опубликована: Сен. 7, 2023

Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy bioproducts. Hybrid aspen tremula × P. alba INRA 717-1B4 is widely used transformation model tree functional genomics biotechnology research. As an outcrossing interspecific hybrid, its genome riddled with sequence polymorphisms which present challenge sequence-sensitive analyses. Here we report telomere-to-telomere this hybrid two chromosome-scale, haplotype-resolved assemblies. We performed comprehensive analysis of the repetitive landscape identified both tandem repeat array-based array-less centromeres. Unexpectedly, most abundant satellite repeats haplotypes lie outside centromeres, consist 147 bp monomer PtaM147, frequently span >1 megabases, form heterochromatic knobs. PtaM147 detected exclusively aspens (section Populus) but PtaM147-like sequences occur LTR-retrotransposons closely related species, suggesting their origin from retrotransposons. The genomic resource generated genotype has greatly improved design editing experiments that highly sensitive to polymorphisms. work should motivate future hypothesis-driven research probe into function aspen-specific DNA.

Язык: Английский

Integrative genomics reveals the polygenic basis of seedlessness in grapevine DOI Creative Commons
Xu Wang, Zhongjie Liu, Fan Zhang

и другие.

Current Biology, Год журнала: 2024, Номер 34(16), С. 3763 - 3777.e5

Опубликована: Авг. 1, 2024

Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and polygenic basis seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative integrative genomics to unravel evolution seedlessness grapes. We generated haplotype-resolved genomes for two seedless cultivars, "Thompson Seedless" (TS, syn. "Sultania") "Black Monukka" (BM). Comparative identified ∼4.25 Mb hemizygous inversion on Chr10 specific with seedless-associated genes VvTT16 VvSUS2 located at breakpoints. Population genomic analyses 548 grapevine accessions revealed distinct clusters identity-by-descent (IBD) results indicated that origin could be traced back "Sultania." Introgression, rather than convergent selection, shaped evolutionary history improvement. Genome-wide association study (GWAS) analysis 110 loci (QTLs) associated 634 candidate genes, including previously unidentified such as three 11S GLOBULIN SEED STORAGE PROTEIN CYTOCHROME P450 well-known like VviAGL11. Integrative resulted 339 core categorized into 13 functional categories related development. Machine learning-based selection achieved remarkable prediction accuracy 97% grapevines. Our findings highlight nature provide molecular genetics an effective

Язык: Английский

Процитировано

11
Mumemto: efficient maximal matching across pangenomes DOI Creative Commons
Vikram S. Shivakumar, Ben Langmead

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 5, 2025

Abstract Aligning genomes into common coordinates is central to pangenome analysis and construction, but it also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts for core genome alignments, helping frame solve the multiple alignment problem. We introduce Mumemto, a tool that computes multi-MUMs other match types across large pangenomes. Mumemto allows visualization of synteny, reveals aberrant assemblies scaffolds, highlights conservation structural variation. 320 human (960GB) in 25.7 hours with under 800 GB memory, over hundreds fungal minutes. implemented C++ Python available open-source at https://github.com/vikshiv/mumemto .

Язык: Английский

Процитировано

1
Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities DOI
Ashutosh Sharma, Nagarjun Vijay

Journal of Molecular Evolution, Год журнала: 2025, Номер unknown

Опубликована: Янв. 17, 2025

Язык: Английский

Процитировано

1
A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity DOI Creative Commons
Temitope Opeyemi Oriowo, Ioannis Chrysostomakis, Sebastián Martín

и другие.

GigaScience, Год журнала: 2025, Номер 14

Опубликована: Янв. 1, 2025

Abstract Background In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads chromosome conformation capture data (Hi-C). Results achieved a haploid size 940 megabase pairs (Mbp) for haplome 1 929 Mbp 2 with high scaffold N50 values 36.4 Mb 36.6 BUSCO scores 96.9% 97.2%, respectively, indicating highly complete assembly. detected notable heterozygosity (1.43%) repeat content (approximately 54%), primarily consisting DNA transposons, which contribute to rearrangements variations. found substantial variations within including insertions, deletions, inversions, translocations. These affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, stress response. annotation protein-coding genes, 30,980 messenger RNAs 23,497 were identified completeness score, further underpins contiguity our assemblies. performed gene family evolution comparing proteome 10 other teleost species, immune system families that prioritize histone-based disease prevention over NB-LRR-related-based responses. Additionally, demographic indicates historical fluctuations effective population P. phoxinus, likely correlating past climatic changes. Conclusions This annotated, phased reference provides crucial resource resolving taxonomic complexity genus Phoxinus highlights importance haplotype-phased assemblies understanding haplotype diversity species characterized heterozygosity.

Язык: Английский

Процитировано

1
The role of centromeric transposable elements in shaping chromosome evolution DOI Creative Commons
Christian Parisod, Manuel Poretti, Terezie Mandáková

и другие.

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Фев. 3, 2025

Abstract Transposable elements (TEs) play pivotal roles in genome evolution, yet their impact on pericentromeric regions of chromosomes, characterized by high sequence turnover and TE abundance, remains largely unclear. This gap knowledge limits our understanding TEs biology role within host genomes. In this study, we address analysing chromosome-scale assemblies to explore the content dynamics four closely related Biscutella species. Although they share substantial synteny, observe significant variability non-coding genome, especially species affected strongest genetic drift due smallest population size. By comparing from CRM clade, which specifically target centromeric regions, with those Athila identify specialized CRMs that follow centromeres after recent repositioning, alongside an invasion copies exhibit less insertion bias. Additionally, find migration towards distal nucleolus organizer correlates increased DNA methylation decreased gene expression. These results highlight how rapid evolution driven bursts activity can significantly functionality stability. Our findings offer new insights into evolutionary mechanisms shaping organization underscore broader implications for adaptation.

Язык: Английский

Процитировано

1
A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks DOI Creative Commons
Drew A. Larson, Margaret Staton, B. G. Kapoor

и другие.

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Фев. 11, 2025

Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that ecologically, culturally, and economically important. We report the first haplotype‐resolved chromosome‐scale genome assembly of Q. conduct comparative analyses structure gene content against other published Fagaceae genomes. investigate genetic diversity this widespread phylogenetic relationships among oaks using whole data. Despite strongly conserved chromosome synteny size , certain families have undergone rapid changes in size, including defense genes. Unbiased annotation resistance (R) genes revealed overall number R similar – as are chromosomal locations clusters but, within more labile. found has high diversity, much which predates its divergence from likely impacts time estimations. Our results highlight discordance genus. The white represents a major new resource for studying evolution . Additionally, we show unbiased key to accurately assessing

Язык: Английский

Процитировано

1
Copy number variation contributes to parallel local adaptation in an invasive plant DOI Creative Commons
Jonathan Wilson, Vanessa C. Bieker,

Lotte van Boheemen

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(10)

Опубликована: Март 3, 2025

Adaptation is a critical determinant of the diversification, persistence, and geographic range limits species. Yet genetic basis adaptation often unknown potentially underpinned by wide mutational types-from single nucleotide changes to large-scale alterations chromosome structure. Copy number variation (CNV) thought be an important source adaptive variation, as indicated decades candidate gene studies that point CNVs underlying rapid strong selective pressures. Nevertheless, population-genomic face unique logistical challenges not encountered other forms variation. Consequently, few have systematically investigated contributions at genome-wide scale. We present analysis CNV contributing invasive weed, Ambrosia artemisiifolia. show clear signatures parallel local between North American (native) European (invaded) ranges, implying widespread reuse during shared heterogeneous patterns selection. used principal component (PCA) genotype regions in whole-genome sequences samples collected over last two centuries. identified 16 large up 11.85 megabases length, eight which signals evolutionary change, with pronounced frequency shifts historic modern populations. Our results provide compelling evidence underlies contemporary timescales natural

Язык: Английский

Процитировано

1
Post-polyploidization centromere evolution in cotton DOI
Yan Hu, Jinlei Han, Shangkun Jin

и другие.

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Март 3, 2025

Язык: Английский

Процитировано

1
The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual DOI Creative Commons
Kuan-Hao Chao, Aleksey V. Zimin, Mihaela Pertea

и другие.

G3 Genes Genomes Genetics, Год журнала: 2023, Номер 13(3)

Опубликована: Янв. 11, 2023

We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. organized sequence into chromosomes and filled in gaps using recently completed T2T-CHM13 as guide, yielding gap-free genome, Han1, containing 3,099,707,698 bases. Using annotation reference, we mapped all genes onto Han1 identified additional gene copies, generating total 60,708 putative genes, which 20,003 are protein-coding. A comprehensive comparison between revealed that 235 protein-coding were substantially different individuals, with frameshifts or truncations affecting sequence. Most these heterozygous variants one copy was unaffected. This represents first gene-level two finished, annotated individual human genomes.

Язык: Английский

Процитировано

18
Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data DOI Creative Commons
Rebecca Serra Mari, Sven Schrinner, Richard Finkers

и другие.

Genome biology, Год журнала: 2024, Номер 25(1)

Опубликована: Янв. 19, 2024

Abstract Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses computational challenge. We introduce novel strategy for genomes present an autotetraploid potato cultivar Altus. Our method uses low-depth sequencing data from offspring population to achieve chromosomal clustering phasing on graph. approach generates high-quality assemblies individual chromosomes with haplotype-specific sequence resolution whole chromosome arms can be applied in common breeding scenarios where collections are available.

Язык: Английский

Процитировано

8