Liu, Z.-Y. | bioRxiv Science

bioRxiv2020

Genome assembly and annotation of Macadamia tetraphylla

Macadamia is a kind of evergreen nut trees which belong to the Proteaceae family. The two commercial macadamia species, Macadamia integrifolia and M. tetraphylla, are highly prized for their edible kernels. Catherine et al. reported M. integrifolia genome using NGS sequencing technology. However, the lack of a high-quality assembly for M. tetraphylla hinders the progress in biological research and breeding program. In this study, we report a high-quality genome sequence of M. tetraphylla using the Oxford Nanopore Technologies (ONT) technology. We generated an assembly of 750.54 Mb with a contig N50 length of 1.18 Mb, which is close to the size estimated by flow cytometry and k-mer analysis. Repetitive sequence represent 58.57% of the genome sequence, which is strikingly higher compared with M. integrifolia. A total of 31,571 protein-coding genes were annotated with an average length of 6,055 bp, of which 92.59% were functionally annotated. The genome sequence of M. tetraphylla will provide novel insights into the breeding of novel strains and genetic improvement of agronomic traits.

genomics↗

bioRxiv2020

Human Influenza A Virus H1N1pdm Full-length Genome Sequencing in USA and Taiwan in 2015-16 Flu Season and Disease Correlation

During the 2015-16 winter, the US experienced a relatively mild influenza season compared to Taiwan which had a higher number of total and severe cases. While H1N1pdm viruses dominated global surveillance efforts that season, the global distribution of genetic variants and their contributions to disease severity have not been investigated. Samples collected from influenza A positive patients by the Johns Hopkins Center of Excellence for Influenza Research and Surveillance (JH-CEIRS) active surveillance in the emergency rooms in Baltimore, Maryland, USA and northern Taiwan between November 2015 and April 2016, were processed for influenza A virus whole genome sequencing. In Baltimore, the majority of the viruses were the H1N1pdm clade 6B.1 and no H1N1pdm clade 6B.2 viruses were detected. In northern Taiwan, more than half of the H1N1pdm viruses were clade 6B.1 and 38% were clade 6B.2, consistent with the global observation that most 6B.2 viruses circulated in Asia and not North America. Whole virus genome sequence analysis identified two genetic subgroups present in each of the 6B.1 and 6B.2 clades and one 6B.1 intraclade reassortant virus. Clinical data showed 6B.2 patients had more disease symptoms including higher crude and inverse probability weighted odds of pneumonia than 6B.1 patients, suggesting 6B.2 circulation may contribute to the severe flu season in Taiwan. Local surveillance efforts linking H1N1pdm virus sequences to patient clinical and demographic data improve our understanding of influenza circulation and disease potential.

microbiology↗