The outbreak of 2019-nCoV in the central Chinese city of Wuhan at the end of 2019 poses unprecedent public health challenges to both China and the rest world 1 . The new coronavirus shares high sequence identity to SARS-CoV and a newly identified bat coronavirus 2 . While bats may be the reservoir host for various coronaviruses, whether 2019-nCoV has other hosts is still ambiguous. In this study, one coronavirus isolated from Malayan pangolins showed 100%, 98.2%, 96.7% and 90.4% amino acid identity with 2019-nCoV in the E, M, N and S genes, respectively. In particular, the receptor-binding domain of the S protein of the Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference. Comparison of available genomes suggests 2019-nCoV might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. Infected pangolins showed clinical signs and histopathological changes, and the circulating antibodies reacted with the S protein of 2019-nCoV.
Pangolins are among the most critically endangered animals due to heavy poaching and world wild trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load.Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diet. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.
Chinese jujube (Ziziphus jujuba Mill) is an economically important fruit species native to China with high nutritious and medicinal value. Genotyping-by-sequencing was used to detect and genotype single nucleotide polymorphisms (SNPs) in a core collection of 150 Chinese jujube accessions and further to characterize their genetic diversity, population structure, and linkage disequilibrium (LD). A total of 4,680 high-quality SNPs were identified, of which 38 sets of tri-allelic SNPs were detected. The average polymorphism information content (PIC) values based on bi-allelic SNPs and tri-allelic SNPs were 0.27 and 0.38, respectively. STRUCTURE and principal coordinate analyses based on SNPs revealed that the 150 accessions could be clustered into two groups. However, neighbor-joining trees indicated the accessions should be grouped into three major clusters. Our data confirm that the resolving power for genetic diversity was similar for the SSRs and SNPs. In contrast, regarding population structure, the resolving power was higher for SSRs than for SNPs. The LD pattern in Chinese jujube was investigated for the first time. We observed a relatively rapid LD decay with a short range (∼10 kb) for all pseudo-chromosomes and for individual pseudo-chromosomes. Our findings provide important information for future genome-wide association analyses and marker-assisted selective breeding of Chinese jujube.
Austropuccinia psidii, originating in South America, is a globally invasive plant pathogen causing rust disease on Myrtaceae. Several biotypes are recognized with the most widely distributed pandemic strain spreading throughout the Asia-Pacific and Oceania regions within the last decade. Austropuccinia psidii has a broad host range (currently 480 myrtaceous species), making it a particularly dangerous plant pathogen. In the nine years since the pandemic biotype was first found in Australia in 2010, the pathogen has caused the near extinction of at least three species, the decline of at least one keystone species, and negatively affected commercial production of several Myrtaceae. To enable molecular and genomic studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype based on PacBio sequence data and scaffolding with Hi-C technology. With an estimated haploid genome size of just over 1 Gbp, it is the largest assembled fungal genome to date. We found the A. psidii genome to have a lower GC content (33.8 %), greatly expanded telomeric and intergenic regions and more repetitive regions (> 90 %) compared to other genomes of species in the Pucciniales, however numbers of predicted coding regions (18,875) are comparable. Most of the increase in genome size is caused by a recent expansion of transposable elements belonging to the Gypsy superfamily. Post-inoculation mRNA sequence capture from a susceptible host provides expression evidence for 10,613 predicted coding genes, including 210 of the 367 putative effectors. The completeness of the genome provides a greatly needed resource for strategic approaches to combat disease spread.3
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