The Winner Takes It All: a single genotype of Kalanchoe ×houghtonii is a global invader DOI Creative Commons
Joan Pere Pascual‐Díaz,

Neus Besolí,

Jordi López‐Pujol

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Abstract Background and Aims Invasive alien plant species pose a global challenge, their impact is amplified by globalisation the accelerating pace of climate change. In mild-climate regions, drought-tolerant invasive plants showing broad environmental tolerance have competitive advantage. One example Kalanchoe × houghtonii (Crassulaceae), popularly known as “mother millions”. It hybrid resulting from interploid cross between K. daigremontiana delagoensis , both native to Madagascar. propagated an ornamental plant, has emerged invader in less than century. Four morphotypes this been identified, with different ploidy levels varying capacities. Here we aim investigate genomic variability behind invasion success . Methods We sampled 57 accessions houghtonii, daigremontiana, closely related taxa, including old herbarium materials, all over world. analysed genome size, chromosome numbers, sequenced whole genome, complete plastome sequence each accession, studied diversity ribosomal RNA genes. also performed detailed phylogenomic study using nuclear BUSCO Key Results Our reveals genetic cytogenetic morphotypes, shows that single tetraploid genotype (morphotype A) dominates populations, emerging first reported clonal capable worldwide colonisation. Morphotype A striking uniformity, high phenotypic plasticity, extremely rates vegetative reproduction, representing “general-purpose genotype”. Conclusions The astonishing reproductive capacity, adaptability speed at which colonising new regions spread highlight importance understanding hybridisation polyploidy ecosystems. findings call for need risk assessments before developing hybrids breeding may exhibit characteristics.

Language: Английский

A pangenome reference of 36 Chinese populations DOI Creative Commons
Yang Gao, Xiaofei Yang, Hao Chen

et al.

Nature, Journal Year: 2023, Volume and Issue: 619(7968), P. 112 - 121

Published: June 14, 2023

Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to pangenome form, but populations of Asian ancestry are underrepresented. Here we present data the first phase Chinese Pangenome Consortium, including collection 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority ethnic groups. With average 30.65× high-fidelity long-read coverage, contiguity N50 more than 35.63 megabases total size 3.01 gigabases, CPC add 189 million base pairs euchromatic polymorphic sequences 1,367 protein-coding gene duplications GRCh38. We identified 15.9 small variants 78,072 structural variants, which 5.9 34,223 were not reported in recently released

Language: Английский

Citations

85
The Born in Guangzhou Cohort Study enables generational genetic discoveries DOI
Shujia Huang, Siyang Liu, Mingxi Huang

et al.

Nature, Journal Year: 2024, Volume and Issue: 626(7999), P. 565 - 573

Published: Jan. 31, 2024

Language: Английский

Citations

19
Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage DOI Creative Commons

Mengge Wang,

Yuguo Huang, Kaijun Liu

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(7)

Published: June 17, 2024

Abstract Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome database encompassing 15,563 individuals from both modern Eurasians, including 919 newly reported individuals, to investigate diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events extensive expansions early middle Neolithic. We identify four major population movements, each associated with technological that shaped landscape. First, expansion East Asians millet farmers Yellow River Basin predominantly carrying O2/D subclades significantly influenced formation Sino-Tibetan people facilitated permanent settlement Tibetan Plateau. Second, dispersal rice Yangtze Valley O1 certain O2 sublineages reshapes makeup southern Han Chinese, as well Tai-Kadai, Austronesian, Hmong-Mien, Austroasiatic people. Third, Neolithic Siberian Q/C originated proliferated among hunter-gatherers on Mongolian Plateau Amur Basin, leaving significant imprint gene pools northern China. Fourth, J/G/R derived western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily northwestern Overall, our research provides comprehensive evidence elucidating impact interactions culturally distinct patterns diversity populations.

Language: Английский

Citations

19
Pilot work of the 10K Chinese People Genomic Diversity Project along the Silk Road suggests a complex east-west admixture landscape and biological adaptations DOI
Guanglin He,

Hongbing Yao,

Shuhan Duan

et al.

Science China Life Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

Language: Английский

Citations

4
Ancient Trans-Species Polymorphism at the Major Histocompatibility Complex in Primates DOI Open Access
Alyssa Lyn Fortier, Jonathan K. Pritchard

Published: Jan. 8, 2025

Classical genes within the Major Histocompatibility Complex (MHC) are responsible for peptide presentation to T cells, thus playing a central role in immune defense against pathogens. These subject strong selective pressures including both balancing and directional selection, resulting exceptional genetic diversity—thousands of alleles per gene humans. Moreover, some appear be shared between primate species, phenomenon known as trans-species polymorphism (TSP) or incomplete lineage sorting, which is rare genome overall. However, despite clinical evolutionary importance MHC diversity, we currently lack full picture evolution. To start addressing this gap, explore variation across species our companion paper (Fortier Pritchard, 2024) here individual genes. We used Bayesian phylogenetic methods determine extent TSP at 17 genes, classical non-classical Class I II find support deep 7 10 including—remarkably—between humans old-world monkeys MHC-DQB1. Despite long-term persistence ancient lineages, additionally observe rapid evolution nucleotides encoding proteins’ peptide-binding domains. The most rapidly-evolving amino acid positions extremely enriched autoimmune infectious disease associations. Together, these results suggest complex forces—arising from differential binding—that drive short-term allelic turnover lineages while also maintaining deeply divergent least 31 million years.

Language: Английский

Citations

2
Comparative studies of 2168 plasma proteins measured by two affinity-based platforms in 4000 Chinese adults DOI Creative Commons
Baihan Wang, Alfred Pozarickij, Mohsen Mazidi

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 21, 2025

Abstract Proteomics offers unique insights into human biology and drug development, but few studies have directly compared the utility of different proteomics platforms. We measured plasma levels 2168 proteins in 3976 Chinese adults using both Olink Explore SomaScan The correlation protein between platforms was modest (median rho = 0.29), with abundance data quality parameters being key factors influencing correlation. For 1694 one-to-one matched reagents, 765 513 had cis -pQTLs, including 400 colocalising -pQTLs. Moreover, 1096 1429 were associated BMI, while 279 154 risk ischaemic heart disease, respectively. Addition to conventional for disease improved C-statistics from 0.845 0.862 (NRI: 12.2%) 0.863 16.4%), These results demonstrate these could inform design interpretation future studies.

Language: Английский

Citations

2
Analyses of rare predisposing variants of lung cancer in 6,004 whole genomes in Chinese DOI Creative Commons
Cheng Wang, Juncheng Dai, Na Qin

et al.

Cancer Cell, Journal Year: 2022, Volume and Issue: 40(10), P. 1223 - 1239.e6

Published: Sept. 15, 2022

Language: Английский

Citations

42
The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay DOI Creative Commons
Si Cheng, Zhe Xu,

Shengzhe Bian

et al.

Cell Discovery, Journal Year: 2023, Volume and Issue: 9(1)

Published: July 21, 2023

Ischemic stroke is a leading cause of global mortality and long-term disability. However, there paucity whole-genome sequencing studies on ischemic stroke, resulting in limited knowledge the interplay between genomic phenotypic variations among affected patients. Here, we outline STROMICS design present first analysis by deeply analyzing 10,241 patients from China. We identified 135.59 million variants, > 42% which were novel. Notable disparities allele frequency observed Chinese other populations for 89 variants associated with risk 10 linked to response medications. investigated population structure participants, generating map genetic selection consisting 31 adaptive signals. The adaption MTHFR rs1801133-G allele, links genetically evaluated VB9 (folate acid) southern patients, suggests gene-specific folate supplement strategy. Through genome-wide association 18 stroke-related traits, discovered novel genetic-phenotypic associations extensive cross-trait pleiotropy at 6 lipid-trait loci therapeutic relevance. Additionally, found that set loss-of-function cysteine-altering causal gene NOTCH3 autosomal dominant disorder CADASIL displayed broad neuro-imaging spectrum. These findings deepen our understanding relationship individual layout clinical phenotype provide foundation future efforts utilize human investigate mechanisms underlying outcomes, discover targets, advance precision medicine.

Language: Английский

Citations

36
Long-term exposure to ambient ozone and cardiovascular diseases: Evidence from two national cohort studies in China DOI Creative Commons
Shuru Liang, Yumeng Chen,

Xiaoli Sun

et al.

Journal of Advanced Research, Journal Year: 2023, Volume and Issue: 62, P. 165 - 173

Published: Aug. 23, 2023

The health effects of ambient ozone have been investigated in many previous studies. However, the long-term exposure to on incidence cardiovascular disease (CVD) remain inconclusive.

Language: Английский

Citations

29
Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations DOI Creative Commons

Qiuxia Sun,

Mengge Wang, Lu Tao

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: March 6, 2024

Abstract Background The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding genetic formation, admixture, adaptive features. Besides, linguistical evidence supported controversial hypothesis origin processes. One hotspot case was Guangxi Pinghua Han people (GPH), whose language significantly similar to dialects but uniparental gene pool phylogenetically associated with indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data 619 four families 56 geographically different populations, which 261 21 distinct were first reported here. Results We identified significant population stratification among ethnolinguistically diverse suggesting differentiated admixture GPH shared more alleles related Zhuang than received northern ancestry relative Zhuang. Admixture models estimates distances showed that had a close relationship TK compared Northern Chinese, supporting hypothesis. Further time demographic history reconstruction formed via between robust signatures lipid metabolisms, such as fatty acid desaturases (FADS) medically relevant loci Mendelian disorder (GJB2) complex diseases. also explored unique selection ethnically linguistically lineages found some signals immune malaria resistance. Conclusions Our analysis illuminated language-related fine-scale structure provided support can explain pattern observed diversity formation GPH. This work presented one comprehensive focused on demographical adaptative process, for personal management disease risk prediction large-scale whole-genome sequencing projects would provide entire landscape southern contributions traits.

Language: Английский

Citations

12