Ips nitidus is a well-known conifer pest that has contributed significantly to spruce forest disturbance in the Qinghai-Tibet Plateau and seriously threatens the ecological balance of these areas. We report a chromosome-level genome of I. nitidus determined by PacBio and Hi-C technology. Phylogenetic inference showed that it diverged from the common ancestor of I. typographus ∼2.27 mya. Gene family expansion in I. nitidus was characterized by DNA damage repair and energy metabolism, which may facilitate adaptation to high-altitude hypoxia. Interestingly, differential gene expression analysis revealed upregulated genes associated with high-altitude hypoxia adaptation and downregulated genes associated with detoxification after feeding and tunneling in fungal symbiont Ophiostoma bicolor-colonized substrates. Our findings provide evidence of the potential adaptability of I. nitidus to conifer host, high-altitude hypoxia and insight into how fungal symbiont assist in this process. This study enhances our understanding of insect adaptation, symbiosis, and pest management.

• Klíčová slova
• Ecology, Genetics, Genomics,
• Publikační typ
• časopisecké články MeSH

Genetic recombination plays a critical role in the emergence of pathogens with phenotypes such as drug resistance, virulence, and host adaptation. Here, we tested the hypothesis that recombination between sympatric ancestral populations leads to the emergence of divergent variants of the zoonotic parasite Cryptosporidium parvum with modified host ranges. Comparative genomic analyses of 101 isolates have identified seven subpopulations isolated by distance. They appear to be descendants of two ancestral populations, IIa in northwestern Europe and IId from southwestern Asia. Sympatric recombination in areas with both ancestral subtypes and subsequent selective sweeps have led to the emergence of new subpopulations with mosaic genomes and modified host preference. Subtelomeric genes could be involved in the adaptive selection of subpopulations, while copy number variations of genes encoding invasion-associated proteins are potentially associated with modified host ranges. These observations reveal ancestral origins of zoonotic C. parvum and suggest that pathogen import through modern animal farming might promote the emergence of divergent subpopulations of C. parvum with modified host preference.

• Klíčová slova
• Cryptosporidium parvum, adaptive selection, emerging infection, genome evolution, population genetics, recombination,
• MeSH
• Cryptosporidium parvum * genetika   MeSH
• Cryptosporidium * genetika   MeSH
• kryptosporidióza * parazitologie   MeSH
• rekombinace genetická MeSH
• variabilita počtu kopií segmentů DNA MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

• Klíčová slova
• adaptive introgression, agronomic traits, genetic diversity, genetic selection, migration, whole-genome sequences,
• MeSH
• genetická variace MeSH
• genom * MeSH
• jednonukleotidový polymorfismus MeSH
• ovce domácí * genetika   MeSH
• ovce genetika   MeSH
• sekvenční analýza DNA MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Asie MeSH
• Evropa MeSH
• Írán MeSH

Tetraparvovirus, formerly known as Partetravirus, is a newly discovered genus in the family Parvoviridae that is considered phylogenetically distinct from other parvoviruses. However, nothing is known about the prevalence of Tetraparvovirus in special livestock living on the Qinghai-Tibet Plateau of China, such as Tibetan pigs and Tibetan sheep. A pair of special primers was designed based on the conserved regions in the genome of ungulate tetraparvovirus 2 (P-PARV4) and ungulate tetraparvovirus 4 (O-PARV4) and was used to detect P-PARV4 in domestic pigs and Tibetan pigs and O-PARV4 in ovines and Tibetan sheep. The results showed a 15.59 and 9.38% prevalence of P-PARV4 in domestic pigs (18.96% in Gansu Province and 11.76% in Qinghai Province) and Tibetan pigs (14.28% in Gansu Province and 4.44% in Qinghai Province), respectively, and a 7.31 and 5.20% prevalence of O-PARV4 in ovines (6.61% in Gansu Province and 8.00% in Qinghai Province) and Tibetan sheep (4.55% in Gansu Province and 5.50% in Qinghai Province), respectively. The prevalence of P-PARV4 was 14.76% (31/210) for ≤1-month-old pigs and 10.58% (20/189) for > 1-month-old pigs, and the positive rates of O-PARV4 were 7.65% (18/235) for ≤1-month-old sheep and 5.05% (11/218) for > 1-month-old sheep. The phylogenetic analysis of NS1, VP1, VP2 and the whole PARV4-related provirus genome demonstrated that both P-PARV4 and O-PARV4 sequences in this study were more closely related to the sequences of other strains discovered in the same genus of animals. The identity analyses for the full-length VP2 genomes of O-PARV4 revealed 98.84-100.00% sequence identity among the 7 strains and the previously reported strain, which was 98.60-99.28% for P-PARV4. In the present study, for the first time, we have provided comprehensive information regarding the widespread infection of P-PARV4 and O-PARV4 in special livestock on the Qinghai-Tibet Plateau in China. Our present findings highlight the importance of epidemiologic surveillance to limit the spread of Tetraparvovirus in livestock at high altitudes in China.

• Klíčová slova
• Qinghai-Tibet plateau, Tibetan pig, Tibetan sheep, Ungulate tetraparvovirus 2, Ungulate tetraparvovirus 4,
• MeSH
• dobytek virologie   MeSH
• fylogeneze MeSH
• genom virový * MeSH
• infekce viry z čeledi Parvoviridae epidemiologie   veterinární   MeSH
• ovce virologie   MeSH
• Parvovirinae genetika   izolace a purifikace   MeSH
• polymerázová řetězová reakce MeSH
• prasata virologie   MeSH
• prevalence MeSH
• sekvenční analýza DNA MeSH
• virové proteiny genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Čína epidemiologie   MeSH
• Tibet epidemiologie   MeSH
• Názvy látek
• virové proteiny MeSH

Porcine deltacoronavirus (PDCoV) is a recently discovered RNA virus that belongs to the family Coronaviridae and genus Deltacoronavirus. This virus causes enteric disease in piglets that is characterized by enteritis and diarrhoea. In our present investigation, 189 diarrhoeic samples were collected between July 2016 and May 2017 from Tibetan pigs inhabiting in three different provinces surrounding the Qinghai-Tibet Plateau of China. We then applied the molecular-based method of reverse transcription polymerase chain reactions (RT-PCRs) to detect the presence of PDCoV in collected samples, and RT-PCR indicated that the prevalence of PDCoV was 3.70% (7/189) in Tibetan pigs. Four of 7 PDCoV-positive pigs were monoinfections of PDCoV, three samples were co-infections of PDCoV with porcine epidemic diarrhoea virus (PEDV), and 52 (27.51%) samples were positive for PEDV. Four strains with different full-length genomes were identified (CHN/GS/2016/1, CHN/GS/2016/2, CHN/GS-/2017/1 and CHN/QH/2017/1), and their genomes were used to analyse the characteristics of PDCoV currently prevalent in Tibetan pigs. We found a 3-nt insertion in the spike gene in four strains in Tibetan pigs. Phylogenetic analysis of the complete genome and spike and nucleocapsid gene sequences revealed that these strains shared ancestors with the strain CHN-AH-2004, which was found in pigs from the Anhui province of China mainland. However, PDCoV strains from Tibetan pigs formed different branches within the same cluster, implying continuous evolution in the field. Our present findings highlight the importance of epidemiologic surveillance to limit the spread of PDCoV in livestock at high altitudes in China.

• Klíčová slova
• China, Qinghai-Tibet Plateau, Tibetan pigs, porcine deltacoronavirus,
• MeSH
• Coronavirus genetika   izolace a purifikace   MeSH
• feces virologie   MeSH
• fylogeneze MeSH
• genom virový genetika   MeSH
• koronavirové infekce diagnóza   epidemiologie   veterinární   virologie   MeSH
• kvantitativní polymerázová řetězová reakce veterinární   MeSH
• nemoci prasat diagnóza   epidemiologie   virologie   MeSH
• prasata virologie   MeSH
• prevalence MeSH
• průjem veterinární   virologie   MeSH
• sekvenční analýza DNA MeSH
• virové proteiny genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Tibet epidemiologie   MeSH
• Názvy látek
• virové proteiny MeSH