Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of food-grade soybean

Long read sequencing has been widely used to detect structure variations that are not captured by short read sequencing in plant genomic research. In this study, we described an analysis of whole genome re-sequencing of 29 soybean varieties using nanopore long-read sequencing. The compiled germplasm reflects diverse applications of food-grade soybeans, including soy milk and tofu production, as well as consumption of natto, sprout, and edamame (vegetable soybean). We have identified 365,497 structural variations in these newly re-sequenced genomes and found that the newly identified structural variations are associated with important agronomic traits. These traits include seed weight, flowering time, plant height, oleic acid content, methionine content, and Kunitz trypsin inhibitor content, all of which significantly impact soybean production, quality, and market value. Experimental validation supports the roles of predicted candidate genes and structural variants in these biological processes. Our research provides a new source for rapid marker discovery in soybean and other crop genomes using structural variation and whole genome sequencing.

Population genomics advances in frontier ethnic minorities in China

China, with its large geographic span, possesses rich genetic diversity across vast frontier regions in addition to the Han Chinese majority. Importantly, demographic events and various natural and cultural environments in Chinese frontier regions have shaped the genomic diversity of ethnic minorities via local adaptations. Thus, insights into the genetic diversity and adaptive evolution of these under-represented ethnic groups are crucial for understanding evolutionary scenarios and biomedical implications in East Asian populations. Here, we focus on ethnic minorities in Chinese frontier regions and review research advances regarding genomic diversity, genetic structure, population history, genetic admixture, and local adaptation. We first provide an overview of the extensive genetic diversity across populations in different Chinese frontier regions. Next, we summarize research progress regarding genetic ancestry, demographic history, the adaptive process, and the archaic identification of multiple ethnic minorities in different Chinese frontier regions. Finally, we discuss the gaps and opportunities in genomic studies of Chinese populations and the need for a more comprehensive understanding of genomic diversity and the evolution of populations of East Asian ancestry in the post-genomic era.

A highland-adaptation variant near MCUR1 reduces its transcription and attenuates erythrogenesis in Tibetans

To identify genomic regions subject to positive selection that might contain genes involved in high-altitude adaptation (HAA), we performed a genome-wide scan by whole-genome sequencing of Tibetan highlanders and Han lowlanders. We revealed a collection of candidate genes located in 30 genomic loci under positive selection. Among them, MCUR1 at 6p23 was a novel pronounced candidate. By single-cell RNA sequencing and comprehensive functional studies, we demonstrated that MCUR1 depletion leads to impairment of erythropoiesis under hypoxia and normoxia. Mechanistically, MCUR1 knockdown reduced mitochondrial Ca2+ uptake and then concomitantly increased cytosolic Ca2+ levels, which thereby reduced erythropoiesis via the CAMKK2-AMPK-mTOR axis. Further, we revealed rs61644582 at 6p23 as an expression quantitative trait locus for MCUR1 and a functional variant that confers an allele-specific transcriptional regulation of MCUR1. Overall, MCUR1-mediated mitochondrial Ca2+ homeostasis is highlighted as a novel regulator of erythropoiesis, deepening our understanding of the genetic mechanism of HAA.

SVLearn: a dual-reference machine learning approach enables accurate cross-species genotyping of structural variants

Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range of human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here, we introduce SVLearn, a machine-learning approach for genotyping bi-allelic SVs. It exploits a dual-reference strategy to engineer a curated set of genomic, alignment, and genotyping features based on a reference genome in concert with an allele-based alternative genome. Using 38,613 human-derived SVs, we show that SVLearn significantly outperforms four state-of-the-art tools, with precision improvements of up to 15.61% for insertions and 13.75% for deletions in repetitive regions. On two additional sets of 121,435 cattle SVs and 113,042 sheep SVs, SVLearn demonstrates a strong generalizability to cross-species genotype SVs with a weighted genotype concordance score of up to 90%. Notably, SVLearn enables accurate genotyping of SVs at low sequencing coverage, which is comparable to the accuracy at 30× coverage. Our studies suggest that SVLearn can accelerate the understanding of associations between the genome-scale, high-quality genotyped SVs and diseases across multiple species.

Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility

Genomic structural variants (SVs) are a major source of genetic diversity in humans. Here, through long-read sequencing of 945 Han Chinese genomes, we identify 111,288 SVs, including 24.56% unreported variants, many with predicted functional importance. By integrating human population-level phenotypic and multi-omics data as well as two humanized mouse models, we demonstrate the causal roles of two SVs: one SV that emerges at the common ancestor of modern humans, Neanderthals, and Denisovans in GSDMD for bone mineral density and one modern-human-specific SV in WWP2 impacting height, weight, fat, craniofacial phenotypes and immunity. Our results suggest that the GSDMD SV could serve as a rapid and cost-effective biomarker for assessing the risk of cisplatin-induced acute kidney injury. The functional conservation from human to mouse and widespread signals of positive natural selection suggest that both SVs likely influence local adaptation, phenotypic diversity, and disease susceptibility across diverse human populations.

Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics

With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics. The goal is to examine the application and progress of resequencing technologies in this field and to consider future developments, including deep learning models and machine learning algorithms, which promise to enhance analytical methodologies and drive further advancements in population genomics.

Genome-wide characterization of structure variations in the Xiang pig for genetic resistance to African swine fever

African swine fever (ASF) is a rapidly fatal viral haemorrhagic fever in Chinese domestic pigs. Although very high mortality is observed in pig farms after an ASF outbreak, clinically healthy and antibody-positive pigs are found in those farms, and viral detection is rare from these pigs. The ability of pigs to resist ASF viral infection may be modulated by host genetic variations. However, the genetic basis of the resistance of domestic pigs against ASF remains unclear. We generated a comprehensive set of structural variations (SVs) in a Chinese indigenous Xiang pig with ASF-resistant (Xiang-R) and ASF-susceptible (Xiang-S) phenotypes using whole-genome resequencing method. A total of 53,589 nonredundant SVs were identified, with an average of 25,656 SVs per individual in the Xiang pig genome, including insertion, deletion, inversion and duplication variations. The Xiang-R group harboured more SVs than the Xiang-S group. The F-statistics (FST) was carried out to reveal genetic differences between two populations using the resequencing data at each SV locus. We identified 2,414 population-stratified SVs and annotated 1,152 Ensembl genes (including 986 protein-coding genes), in which 1,326 SVs might disturb the structure and expression of the Ensembl genes. Those protein-coding genes were mainly enriched in the Wnt, Hippo, and calcium signalling pathways. Other important pathways associated with the ASF viral infection were also identified, such as the endocytosis, apoptosis, focal adhesion, Fc gamma R-mediated phagocytosis, junction, NOD-like receptor, PI3K-Akt, and c-type lectin receptor signalling pathways. Finally, we identified 135 candidate adaptive genes overlapping 166 SVs that were involved in the virus entry and virus-host cell interactions. The fact that some of population-stratified SVs regions detected as selective sweep signals gave another support for the genetic variations affecting pig resistance against ASF. The research indicates that SVs play an important role in the evolutionary processes of Xiang pig adaptation to ASF infection.

Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds

BACKGROUND

Mutton quality is closely related to genetic variants and gene expression alterations during growth and development, resulting in differences in nutritional values, flavor, and odor.

RESULTS

We first evaluated and compared the composition of crude protein, crude fat, cholesterol, amino acid (AA), and fatty acid (FA) in the longissimus dorsi muscle of Guizhou black goats (GZB, n = 5) and Yunshang black goats (YBG, n = 6). The contents of cholesterol and FA related to odor in GZB were significantly lower than that in YBG, while the concentrations of umami amino acids and intramuscular fat were significantly higher in GZB. Furthermore, structural variants (SVs) in the genomes of GZB (n = 30) and YBG (n = 11) were explored. It was found that some regions in Chr 10/12/18 were densely involved with a large number of SVs in the genomes of GZB and YBG. By setting FST ≥ 0.25, we got 837 stratified SVs, of which 25 SVs (involved in 12 genes, e.g., CORO1A, CLIC6, PCSK2, and TMEM9) were limited in GZB. Functional enrichment analysis of 14 protein-coding genes (e.g., ENPEP, LIPC, ABCA5, and SLC6A15) revealed multiple terms and pathways related with metabolisms of AA, FA, and cholesterol. The SVs (n = 10) obtained by the whole genome resequencing were confirmed in percentages of 36.67 to 86.67% (n = 96) by PCR method. The SVa and SVd polymorphisms indicated a moderate negative correlation with HMGCS1 activity (n = 17).

CONCLUSION

This study is the first to comprehensively reveal potential SVs related to mutton nutritional values, flavor, and odor based on genomic compare between two black goat breeds with closely genetic relationship. The SVs generated in this study provide a data resource for deeper studies to understand the genomic characteristics and possible evolutionary outcomes with better nutritional values, flavor and extremely light odor.

Introgression drives adaptation to the plateau environment in a subterranean rodent

BACKGROUND

Introgression has repeatedly been shown to play an important role in the adaptation of species to extreme environments, yet how introgression enables rodents with specialized subterranean lifestyle to acclimatize to high altitudes is still unclear. Myospalacinae is a group of subterranean rodents, among which the high-altitude plateau zokors (Eospalax baileyi) and the low-altitude Gansu zokors (E. cansus) are sympatrically distributed in the grassland ecosystems of the Qinghai-Tibet Plateau (QTP). Together, they provide a model for the study of the role of introgression in the adaptation of low-altitude subterranean rodents to high altitudes.

RESULTS

Applying low-coverage whole-genome resequencing and population genetics analyses, we identified evidence of adaptive introgression from plateau zokors into Gansu zokors, which likely facilitated the adaptation of the latter to the high-altitude environment of the QTP. We identified positively selected genes with functions related to energy metabolism, cardiovascular system development, calcium ion transport, and response to hypoxia which likely made critical contributions to adaptation to the plateau environment in both plateau zokors and high-altitude populations of Gansu zokors.

CONCLUSIONS

Introgression of genes associated with hypoxia adaptation from plateau zokors may have played a role in the adaptation of Gansu zokors to the plateau environment. Our study provides new insights into the understanding of adaptive evolution of species on the QTP and the importance of introgression in the adaptation of species to high-altitude environments.

Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer

Cancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the mechanisms underlying the formation of these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are a rich source of enhancers displaying cancer-specific activity. In colorectal cancer and other epithelial tumors, oncogenic MAPK/AP1 signaling drives the activation of enhancers derived from the primate-specific ERV family LTR10. Functional studies in colorectal cancer cells revealed that LTR10 elements regulate tumor-specific expression of multiple genes associated with tumorigenesis, such as ATG12 and XRCC4. Within the human population, individual LTR10 elements exhibit germline and somatic structural variation resulting from a highly mutable internal tandem repeat region, which affects AP1 binding activity. Our findings reveal that ERV-derived enhancers contribute to transcriptional dysregulation in response to oncogenic signaling and shape the evolution of cancer-specific regulatory networks.

Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations

BACKGROUND

A large number of challenging medically relevant genes (CMRGs) are situated in complex or highly repetitive regions of the human genome, hindering comprehensive characterization of genetic variants using next-generation sequencing technologies. In this study, we employed long-read sequencing technology, extensively utilized in studying complex genomic regions, to characterize genetic alterations, including short variants (single nucleotide variants and short insertions and deletions) and copy number variations, in 370 CMRGs across 41 individuals from 19 global populations.

RESULTS

Our analysis revealed high levels of genetic variants in CMRGs, with 68.73% exhibiting copy number variations and 65.20% containing short variants that may disrupt protein function across individuals. Such variants can influence pharmacogenomics, genetic disease susceptibility, and other clinical outcomes. We observed significant differences in CMRG variation across populations, with individuals of African ancestry harboring the highest number of copy number variants and short variants compared to samples from other continents. Notably, 15.79% to 33.96% of short variants were exclusively detectable through long-read sequencing. While the T2T-CHM13 reference genome significantly improved the assembly of CMRG regions, thereby facilitating variant detection in these regions, some regions still lacked resolution.

CONCLUSION

Our results provide an important reference for future clinical and pharmacogenetic studies, highlighting the need for a comprehensive representation of global genetic diversity in the reference genome and improved variant calling techniques to fully resolve medically relevant genes.

Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep

Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated β-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin-O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

Polymorphic transposable elements provide new insights on high-altitude adaptation in the Tibetan Plateau

Several studies demonstrated that populations living in the Tibetan plateau are genetically and physiologically adapted to high-altitude conditions, showing genomic signatures ascribable to the action of natural selection. However, so far most of them relied solely on inferences drawn from the analysis of coding variants and point mutations. To fill this gap, we focused on the possible role of polymorphic transposable elements in influencing the adaptation of Tibetan and Sherpa highlanders. To do so, we compared high-altitude and middle/low-lander individuals of East Asian ancestry by performing in silico analyses and differentiation tests on 118 modern and ancient samples. We detected several transposable elements associated with high altitude, which map genes involved in cardiovascular, hematological, chem-dependent and respiratory conditions, suggesting that metabolic and signaling pathways taking part in these functions are disproportionately impacted by the effect of environmental stressors in high-altitude individuals. To our knowledge, our study is the first hinting to a possible role of transposable elements in the adaptation of Tibetan and Sherpa highlanders.

Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles

Nonreference sequences (NRSs) are DNA sequences present in global populations but absent in the current human reference genome. However, the extent and functional significance of NRSs in the human genomes and populations remains unclear. Here, we de novo assembled 539 genomes from five genetically divergent human populations using long-read sequencing technology, resulting in the identification of 5.1 million NRSs. These were merged into 45284 unique NRSs, with 29.7% being novel discoveries. Among these NRSs, 38.7% were common across the five populations, and 35.6% were population specific. The use of a graph-based pangenome approach allowed for the detection of 565 transcript expression quantitative trait loci on NRSs, with 426 of these being novel findings. Moreover, 26 NRS candidates displayed evidence of adaptive selection within human populations. Genes situated in close proximity to or intersecting with these candidates may be associated with metabolism and type 2 diabetes. Genome-wide association studies revealed 14 NRSs to be significantly associated with eight phenotypes. Additionally, 154 NRSs were found to be in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the understanding of human NRSs and provides novel insights into their functions, facilitating evolutionary and biomedical researches.

Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors

Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.

Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing

Structural variants (SVs), accounting for a larger fraction of the genome than SNPs/InDels, are an important pool of genetic variation, enabling environmental adaptations. Here, we perform long-read sequencing data of 320 Tibetan and Han samples and show that SVs are highly involved in high-altitude adaptation. We expand the landscape of global SVs, apply robust models of selection and population differentiation combining SVs, SNPs and InDels, and use epigenomic analyses to predict enhancers, target genes and biological functions. We reveal diverse Tibetan-specific SVs affecting the regulatory circuitry of biological functions, including the hypoxia response, energy metabolism and pulmonary function. We find a Tibetan-specific deletion disrupts a super-enhancer and downregulates EPAS1 using enhancer reporter, cellular knock-out and DNA pull-down assays. Our study expands the global SV landscape, reveals the role of gene-regulatory circuitry rewiring in human adaptation, and illustrates the diverse functional roles of SVs in human biology.

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

BACKGROUND

During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted.

RESULTS

Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. CONCLUSIONS: We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment

BACKGROUND

Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle.

RESULTS

In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle.

CONCLUSIONS

Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.

A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species

Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.

Genomic structural variation: A complex but important driver of human evolution

Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans

BACKGROUND

Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes.

RESULTS

Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai-Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects.

CONCLUSIONS

Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.

Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Structural variations (SVs) have long been described as being involved in the origin, adaption, and domestication of species. However, the underlying genetic and genomic mechanisms are poorly understood. Here, we report a high-quality genome assembly of Gossypium barbadense acc. Tanguis, a landrace that is closely related to formation of extra-long-staple (ELS) cultivated cotton. An SV-based pan-genome (Pan-SV) was then constructed using a total of 182 593 non-redundant SVs, including 2236 inversions, 97 398 insertions, and 82 959 deletions from 11 assembled genomes of allopolyploid cotton. The utility of this Pan-SV was then demonstrated through population structure analysis and genome-wide association studies (GWASs). Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an SV-based GWAS, certain SVs responsible for speciation, domestication, and improvement in tetraploid cottons were identified. Importantly, some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS. In particular, a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G. barbadense. Collectively, this study provides new insights into genome-wide, gene-scale SVs linked to important agronomic traits in a major crop species and highlights the importance of SVs during the speciation, domestication, and improvement of cultivated crop species.

Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs

Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.

Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.

Analysis of dog breed diversity using a composite selection index

During breed development, domestic dogs have undergone genetic bottlenecks and sustained selective pressures, as a result distinctive genomic diversity occurs to varying degrees within and between breed groups. This diversity can be identified using standard methods or combinations of these methods. This study explored the application of a combined selection index, composite selection signals (CSS), derived from multiple methods to an existing genotype dataset from three breed groups developed in distinct regions of Asia: Qinghai-Tibet plateau dogs (adapted to living at altitude), Xi dogs (with superior running ability) and Mountain hounds (used for hunting ability). The CSS analysis confirmed top ranked genomic regions on CFA10 and CFA21 in Qinghai-Tibet plateau dogs, CFA1 in Xi dogs and CFA5 in Mountain hounds. CSS analysis identified additional significant genomic regions in each group, defined by a total of 1,397, 1,475 and 1,675 significant SNPs in the Qinghai-Tibetan Plateau dogs, Xi dogs and Mountain hounds, respectively. Chitinase 3 Like 1 (CHI3L1) and Leucine Rich Repeat Containing G Protein-Coupled Receptor 6 (LGR6) genes were located in the top ranked region on CFA7 (0.02-1 Mb) in the Qinghai-Tibetan Plateau dogs. Both genes have been associated with hypoxia responses or altitude adaptation in humans. For the Xi dogs, the top ranked region on CFA25 contained the Transient Receptor Potential Cation Channel Subfamily C Member 4 (TRPC4) gene. This calcium channel is important for optimal muscle performance during exercise. The outstanding signals in the Mountain dogs were on CFA5 with 213 significant SNPs that spanned genes involved in cardiac development, sight and generation of biochemical energy. These findings support the use of the combined index approach for identifying novel regions of genome diversity in dogs. As with other methods, the results do not prove causal links between these regions and phenotypes, but they may assist in focusing future studies that seek to identify functional pathways that contribute to breed diversity.

Comparison of Cardiorespiratory Fitness of Chinese Tibetan Adolescents with Their Han Counterparts: A Cross-Sectional Retrospective Study

Cardiorespiratory fitness (CRF) is a core element of healthy physical fitness. Foreign attention to CRF in adolescents at different altitudes is high, while less research has been conducted on Chinese adolescents. In order to compare the CRF of Chinese Tibetan adolescents with their Han counterparts born and raised at high altitude and Chinese Han adolescents at sea level. A total of 2748 participants, including Chinese Tibetan adolescents, Chinese Han adolescents born and raised at high altitudes, and Chinese Han adolescents at sea level aged 12-18 years old, were obtained using convenience sampling and random cluster sampling. The method of the 20 m shuttle run test (20 m SRT) test was used to derive VO_2max by equation. One-way ANOVA and LSD methods were conducted, and effect sizes were calculated to compare the CRF of the three types of adolescents. Regression analysis was used to analyze the relationship between altitude and VO_2max. The VO_2max scores of Chinese Tibetan adolescents and Chinese Han adolescents at sea level were higher than Chinese Han adolescents born and raised at high altitudes. For both boys and girls, the VO_2max scores of Chinese Tibetan adolescents exceeded Chinese Han adolescents at sea level after the age of 16 years old. Regression analysis showed that altitude was inversely associated with VO_2max. The pace of lung growth may distinguish Chinese Tibetan adolescents from Chinese Han adolescents born and raised at high altitudes. The results of the study suggest that we should focus on the changes in CRF in adolescents at different altitudes and should adopt different CRF interventions for adolescents at different altitudes.

Recent advances and current challenges in population genomics of structural variation in animals and plants

The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of studies suggest that SVs of all types and sizes may have a large effect on phenotype and consequently major impact on rapid adaptation, population divergence, and speciation. However, the functional effect of the vast majority of SVs is unknown and the field generally lacks evidence on the phenotypic consequences of most SVs that are suggested to have adaptive potential. Non-human genomes are heavily under-represented in population-scale studies of SVs. We argue that more research on other species is needed to objectively estimate the contribution of SVs to evolution. We discuss technical challenges associated with SV detection and outline the most recent advances towards more representative reference genomes, which opens a new era in population-scale studies of structural variation.

Markhor-derived Introgression of a Genomic Region Encompassing PAPSS2 Confers High-altitude Adaptability in Tibetan Goats

Understanding the genetic mechanism of how animals adapt to extreme conditions is fundamental to determine the relationship between molecular evolution and changing environments. Goat is one of the first domesticated species and has evolved rapidly to adapt to diverse environments, including harsh high-altitude conditions with low temperature and poor oxygen supply but strong ultraviolet radiation. Here, we analyzed 331 genomes of domestic goats and wild caprid species living at varying altitudes (high > 3000 m above sea level and low < 1200 m), along with a reference-guided chromosome-scale assembly (contig-N50: 90.4 Mb) of a female Tibetan goat genome based on PacBio HiFi long reads, to dissect the genetic determinants underlying their adaptation to harsh conditions on the Qinghai-Tibetan Plateau (QTP). Population genomic analyses combined with genome-wide association studies (GWAS) revealed a genomic region harboring the 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (PAPSS2) gene showing strong association with high-altitude adaptability (PGWAS = 3.62 × 10-25) in Tibetan goats. Transcriptomic data from 13 tissues revealed that PAPSS2 was implicated in hypoxia-related pathways in Tibetan goats. We further verified potential functional role of PAPSS2 in response to hypoxia in PAPSS2-deficient cells. Introgression analyses suggested that the PAPSS2 haplotype conferring the high-altitude adaptability in Tibetan goats originated from a recent hybridization between goats and a wild caprid species, the markhor (Capra falconeri). In conclusion, our results uncover a hitherto unknown contribution of PAPSS2 to high-altitude adaptability in Tibetan goats on QTP, following interspecific introgression and natural selection.

QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes

Deciphering the fine-scale molecular mechanisms that shape the genetic effects at disease-associated loci from genome-wide association studies (GWAS) remains challenging. The key avenue is to identify the essential molecular phenotypes that mediate the causal variant and disease under particular biological conditions. Therefore, integrating GWAS signals with context-specific quantitative trait loci (QTLs) (such as different tissue/cell types, disease states, and perturbations) from extensive molecular phenotypes would present important strategies for full understanding of disease genetics. Via persistent curation and systematic data processing of large-scale human molecular trait QTLs (xQTLs), we updated our previous QTLbase database (now QTLbase2, http://mulinlab.org/qtlbase) to comprehensively analyze and visualize context-specific QTLs across 22 molecular phenotypes and over 95 tissue/cell types. Overall, the resource features the following major updates and novel functions: (i) 960 more genome-wide QTL summary statistics from 146 independent studies; (ii) new data for 10 previously uncompiled QTL types; (iii) variant query scope expanded to fit 195 QTL datasets based on whole-genome sequencing; (iv) supports filtering and comparison of QTLs for different biological conditions, such as stimulation types and disease states; (v) a new linkage disequilibrium viewer to facilitate variant prioritization across tissue/cell types and QTL types.

Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology

Long-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T lymphocytes, which can be established efficiently in a biobank to stably supply high-grade genomic DNA sufficiently. We conducted nanopore sequencing of 333 individuals constituting 111 trios with high-coverage long-read sequencing data (depth 22.2x, N50 of 25.8 kb) and identified 74,201 SVs. Our trio-based analysis revealed that more than 95% of the SVs were concordant with Mendelian inheritance. We also identified SVs associated with clinical phenotypes, all of which appear to be stably transmitted from parents to offspring. Our data provide a catalog of SVs in the general Japanese population, and the applied approach using the activated T-lymphocyte resource will contribute to biobank-based human genetic studies focusing on SVs at the population scale.

Long-read sequencing on activated T-cells from a sample of 333 Japanese individuals (representing 111 parent-offspring trios) provides a useful reference dataset of structural variation in the Japanese population.

Human follicular mites: Ectoparasites becoming symbionts

Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans tha continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic or endosymbiotic lifestyle. Somatic nuclei show underreplication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

Population Structure and Genetic Diversity of Chinese Honeybee (Apis Cerana Cerana) in Central China

Central China has a rich terrain with a temperate monsoon climate and varied natural environments for the Chinese honeybee (Apis cerana cerana). However, little comprehensive research on population genetic diversity has been done in this area. A population survey of the structure and genetic diversity of Apis cerana cerana in this area is deeply needed for understanding adaptation to variable environments and providing more references for the protection of honeybee biodiversity. In this study, we present a dataset of 72 populations of Chinese honeybees collected from nine sites by whole genome sequencing in Central China. We obtained 2,790,214,878 clean reads with an average covering a depth of 22×. A total of 27,361,052 single nucleotide polymorphisms (SNPs) were obtained by mapping to the reference genome with an average mapping rate of 93.03%. Genetic evolution analysis was presented via the population structure and genetic diversity based on the datasets of SNPs. It showed that Apis cerana cerana in plains exhibited higher genetic diversity than in mountain areas. The mantel test between Apis cerana cerana groups revealed that some physical obstacles, especially the overurbanization of the plains, contributed to the differentiation. This study is conducive to elucidating the evolution of Apis cerana in different environments and provides a theoretical basis for investigating and protecting the Chinese honeybee.

Population-scale genotyping of structural variation in the era of long-read sequencing

Population-scale studies of structural variation (SV) are growing rapidly worldwide with the development of long-read sequencing technology, yielding a considerable number of novel SVs and complete gap-closed genome assemblies. Herein, we highlight recent studies using a hybrid sequencing strategy and present the challenges toward large-scale genotyping for SVs due to the reference bias. Genotyping SVs at a population scale remains challenging, which severely impacts genotype-based population genetic studies or genome-wide association studies of complex diseases. We summarize academic efforts to improve genotype quality through linear or graph representations of reference and alternative alleles. Graph-based genotypers capable of integrating diverse genetic information are effectively applied to large and diverse cohorts, contributing to unbiased downstream analysis. Meanwhile, there is still an urgent need in this field for efficient tools to construct complex graphs and perform sequence-to-graph alignments.

Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods

Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance to repeats. Improved characterization of SVs can provide more advanced insight into complex traits. With the availability of long-read sequencing, it has become feasible to uncover the full range of SVs. Here, we sequenced one cattle individual using 10× Genomics (10 × G) linked read, Pacific Biosciences (PacBio) continuous long reads (CLR) and circular consensus sequencing (CCS), as well as Oxford Nanopore Technologies (ONT) PromethION. We evaluated the ability of various methods for SV detection. We identified 21,164 SVs, which amount to 186 Mb covering 7.07% of the whole genome. The number of SVs inferred from long-read-based inferences was greater than that from short reads. The PacBio CLR identified the most of large SVs and covered the most genomes. SVs called with PacBio CCS and ONT data showed high uniformity. The one with the most overlap with the results obtained by short-read data was PB CCS. Together, we found that long reads outperformed short reads in terms of SV detections.

Ethnic Specificity of Species and Strain Composition of Lactobacillus Populations From Mother–Infant Pairs, Uncovered by Multilocus Sequence Typing

The maternal gut is thought to be the principal source of potential probiotic bacteria in the infant gut during the lactation stage. It is not clear whether facultative symbiont lactobacilli strictly follow vertical transmission from mother to infant and display the ethnic specificity in terms of species and strain composition in mother–infant cohorts. In the present study, a total of 16 former Lactobacillus species (365 strains) and 11 species (280 strains) were retrieved from 31 healthy mother–infant pairs of two ethnic groups, which have never intermarried, respectively. The result showed that the composition and number of Lactobacillus species between the two ethnic groups varied. Among 106 Lacticaseibacillus paracasei strains isolated, 64 representative strains were classified into 27 sequence types (ST) by means of multilocus sequence typing (MLST), of which 20 STs derived from 33 Uighur strains and 7 STs from 31 Li strains, and no homologous recombination event of genes was detected between strains of different ethnic groups. A go-EBURST analysis revealed that except for a few mother–infant pairs in which more than one STs were detected, L. paracasei isolates from the same mother–infant pair were found to be monophyletic in most cases, confirming vertical transfer of Lactobacillus at the strain level. More notably, L. paracasei isolates from the same ethnic group were more likely than strains from another to be incorporated into a specific phylogenetic clade or clonal complex (CC) with similar metabolic profile of glycan, supporting the hypothesis of ethnic specificity to a large degree. Our study provides evidence for the development of personalized probiotic tailored to very homogenous localized populations from the perspective of maternal and child health.

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing has improved the sensitivity of structural variant discovery. Here, we conduct the long-read sequencing-based structural variant analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We discover a landscape of 132,312 nonredundant structural variants, of which 45.2% are novel. The identified structural variants are of high-quality, with an estimated false discovery rate of 3.2%. The concatenated length of all the structural variants is approximately 13.2% of the human reference genome. We annotate 1,929 loss-of-function structural variants affecting the coding sequence of 1,681 genes. We discover rare deletions in HBA1/HBA2/HBB associated with anemia. Furthermore, we identify structural variants related to immunity which differentiate the northern and southern Chinese populations. Our study describes the landscape of structural variants in the Chinese population and their contribution to phenotypes and disease.

Harnessing the power of multi-omics data for predicting climate change response

Predicting how species will respond to future climate change is of central importance in the midst of the global biodiversity crisis, and recent work has demonstrated the utility of population genomics for improving these predictions. Here, we suggest a broadening of the approach to include other types of genomic variants that play an important role in adaptation, like structural (e.g. copy number variants) and epigenetic variants (e.g. DNA methylation). These data could provide additional power for forecasting response, especially in weakly structured or panmictic species. Incorporating structural and epigenetic variation into estimates of climate change vulnerability, or maladaptation, may not only improve prediction power but also provide insight into the molecular mechanisms underpinning species' response to climate change.