Genetic Characterization and Variation of African Swine Fever Virus China/GD/2019 Strain in Domestic Pigs

African swine fever (ASF) was first introduced into Northern China in 2018 and has spread through China since then. Here, we extracted the viral DNA from the blood samples from an ASF outbreak farm in Guangdong province, China and sequenced the whole genome. We assembled the full length genomic sequence of this strain, named China/GD/2019. The whole genome was 188,642 bp long (terminal inverted repeats and loops were not sequenced), encoding 175 open reading frames (ORF). The China/GD/2019 strain belonged to p72 genotype II and p54 genotype IIa. Phylogenetic analysis relationships based on single nucleotide polymorphisms (SNPs) also demonstrated that it grouped into genotype II. A certain number of ORFs mainly belonging to multigene families (MGFs) were absent in the China/GD/2019 strain in comparison to the China/ASFV/SY-18 strain. A deletion of approximately 1 kb was found in the China/GD/2019 genome which was located at the EP153R and EP402R genes in comparison to the China/2018/AnhuiXCGQ strain. We revealed a synonymous mutation site at gene F317L and a non-synonymous mutation site at gene MGF_360-6L in China/GD/2019 comparing to three known Chinese strains. Pair-wise comparison revealed 165 SNP sites in MGF_360-1L between Estonia 2014 and the China/GD/2019 strain. Comparing to China/GD/2019, we revealed a base deletion located at gene D1133L in China/Pig/HLJ/2018 and China/DB/LN/2018, which results in a frameshift mutation to alter the encoding protein. Our findings indicate that China/GD/2019 is a new variant with certain deletions and mutations. This study deepens our understanding of the genomic diversity and genetic variation of ASFV.

Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity

Pseudomonas stutzeri is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 P. stutzeri complex genomes covering at least six well-defined species among all sequenced Pseudomonas genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the P. stutzeri complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster (ect) was present in all genomes of P. stutzeri species complex strains but distributed at very low frequency (43 out of 9548) in other Pseudomonas genomes, suggesting a possible origin of the ancestors of P. stutzeri species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the P. stutzeri complex, shedding new light on its genomic diversity and evolutionary history.

Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group

Viruses play critical roles in influencing biogeochemical cycles and adjusting host mortality, population structure, physiology, and evolution in the ocean. Marine viral communities are composed of numerous genetically distinct subfamily/genus-level viral groups. Among currently identified viral groups, the HMO-2011-type group is known to be dominant and broadly distributed. However, only four HMO-2011-type cultivated representatives that infect marine SAR116 and Roseobacter strains have been reported to date, and the genetic diversity, potential hosts, and ecology of this group remain poorly elucidated. Here, we present the genomes of seven HMO-2011-type phages that were isolated using four Roseobacter strains and one SAR11 strain, as well as additional 207 HMO-2011-type metagenomic viral genomes (MVGs) identified from various marine viromes. Phylogenomic and shared-gene analyses revealed that the HMO-2011-type group is a subfamily-level group comprising at least 10 discernible genus-level subgroups. Moreover, >2000 HMO-2011-type DNA polymerase sequences were identified, and the DNA polymerase phylogeny also revealed that the HMO-2011-type group contains diverse subgroups and is globally distributed. Metagenomic read-mapping results further showed that most HMO-2011-type phages are prevalent in global oceans and display distinct geographic distributions, with the distribution of most HMO-2011-type phages being associated with temperature. Lastly, we found that members in subgroup IX, represented by pelagiphage HTVC033P, were among the most abundant HMO-2011-type phages, which implies that SAR11 bacteria are crucial hosts for this viral group. In summary, our findings substantially expand current knowledge regarding the phylogenetic diversity, evolution, and distribution of HMO-2011-type phages, highlighting HMO-2011-type phages as major ecological agents that can infect certain key bacterial groups.

The genomic landscape of contemporary western Remote Oceanians

The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands around 3,200 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet, there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous admixture events that occurred around 1,700-2,300 years ago, indicating a peopling history common to all the archipelago. However, our analyses reveal that the Papuan population turnover was geographically uneven, and that the genetic contribution of Papuan-related peoples was male-biased. Furthermore, we detect Polynesian ancestry arriving around 600-1,000 years ago to South Vanuatu, and map its distribution to both Polynesian- and non-Polynesian-speaking islands. Lastly, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.

Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec

The loss of genetic diversity is a challenge many species are facing, and genomics is a potential tool that can inform and prioritize decision making. Caribou populations have experienced significant recent declines throughout Québec, Canada, and some are considered threatened or endangered. We calculated the ancestral and contemporary patterns of genomic diversity of five caribou populations and applied a comparative framework to assess the interplay between demography and genomic diversity. We calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates. Whole genome re-sequencing was completed on 67 caribou and genotype likelihoods were estimated. We calculated nucleotide diversity, θπ and estimated the coalescent or ancestral Ne, which ranged from 12,030 to 15,513. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary Ne:NC ratio. Importantly, conservation genetics theory would predict this population to be of less concern based on this ratio. Of note, F varied only slightly between populations, and runs of homozygosity were not abundant in the genome. Our study highlights how genomic patterns are nuanced and misleading if viewed only through a contemporary lens; a holistic view should integrate ancestral Ne and Tajima’s D into conservation decisions.

Yeast Hybrids in Brewing

: Microbiology has long been a keystone in fermentation and the utilization of yeast biology rein-forces molecular biotechnology as the pioneering frontier in brewing science. Consequently, modern understanding of the brewer’s yeast has faced significant refinement over the last few decades. This publication presents a condensed summation of Saccharomyces species dynamics with an emphasis on the relationship between traditional ale yeast, Saccharomyces cerevisiae, and the interspecific hybrids used in lager beer production, S. pastorianus. Introgression from other Sac-charomyces species is also touched on. The unique history of Saccharomyces cerevisiae and Saccharo-myces hybrids are exemplified by recent genomic sequencing studies aimed at categorizing brewing strains through phylogeny and redefining Saccharomyces species boundaries. Phylogenetic investigations highlight the genomic diversity of Saccharomyces cerevisiae ale strains long known to brewers by their fermentation characteristics and phenotypes. Discoveries of genomic contribu-tions from interspecific Saccharomyces species into the genome of S. cerevisiae strains is ever more apparent with increased investigations on the hybrid nature of modern industrial and historical fermentation yeast.

Genomic Insights Into the Population History and Biological Adaptation of Southwestern Chinese Hmong–Mien People

Hmong–Mien (HM) -speaking populations, widely distributed in South China, the north of Thailand, Laos, and Vietnam, have experienced different settlement environments, dietary habits, and pathogenic exposure. However, their specific biological adaptation remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are also unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations; one localized in the HM clines, and others possessed affinity with Han Chinese. We also identified one new ancestral lineage specifically existed in HM people, which spatially distributed from Sichuan and Guizhou in the north to Thailand in the south. The sharing patterns of the newly identified homogenous ancestry component combined the estimated admixture times via the decay of linkage disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward in the historic period, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese Population Genomic Diversity Project (CPGDP), especially in the regions with rich ethnolinguistic diversity.

Genome structure and diversity among Cynanchum wilfordii accessions

Background Cynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information. Results We collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events. Conclusions Cw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.