Intercontinental transmission and local demographic expansion of SARS-CoV-2.

The global outbreak of coronavirus disease 2019 (COVID-19) is greatly threatening the public health in the world. We reconstructed global transmissions and potential demographic expansions of severe acute respiratory syndrome coronavirus 2 based on genomic information. We found that intercontinental transmissions were rare in January and early February but drastically increased since late February. After world-wide implements of travel restrictions, the transmission frequencies decreased to a low level in April. We identified a total of 88 potential demographic expansions over the world based on the star-radiative networks and 75 of them were found in Europe and North America. The expansion numbers peaked in March and quickly dropped since April. These findings are highly concordant with epidemic reports and modelling results and highlight the significance of quarantine validity on the global spread of COVID-19. Our analyses indicate that the travel restrictions and social distancing measures are effective in containing the spread of COVID-19.

A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa.

Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.

[Research on growth characteristic of Scirpus yagara Ohw and its decomposition on the riparian zone].

In order to understand growth of plant and its effect on ecological restoration of riparian zone, pilot-scale Scirpus yagara Ohw riparian zone had been studied for one year. Height and density of Scirpus yagara Ohw in different water depth showed that the water depth endurance of Scirpus yagara Ohw was not strong, and it growed and germinated better in shallow water. Contrast between harvest area and without harvest area showed that harvest was good for germination and growth of Scirpus yagara Ohw in next year. Distribution of biomass and N and P fixation between the underground and overground Scirpus yagara Ohw showed that N and P fixation of the underground was 50% and 126% more than that of the overground, respectively. Harvest of the overground Scirpus yagara Ohw can remove 40.5% of the total N and 30.6% of the total P. Dunked in water for 130 days, the overground Scirpus yagara Ohw lose 27.10% of its dry weight, 40.80% of the total N and 76.80% of tha total P. And the released pollutants have no serious cumulation in water.

[Pilot-scale study on riparian mixed plant zones treating polluted river water].

The polluted river water is treated with pilot-scale riparian zones of no aquatic plant, Vetiveria zizanioides + submerged plants, and weed+ Typha angustifolia L. + Phragmites communis. It is shown that the vegetation water zones are better than the no vegetation water zone and Vetiveria zizanioides + submerged plants zone is the best in improving water quality. The average removals of the Vetiveria zizanioides + submerged plant zone is 43.5% COD, 71.1% ammonia and 69.3% total phosphorus respectively. The dissolved oxygen (DO) and temperature of effluents from the three water zones are also investigated. It shows that DO of effluent from the vegetation zones are more stable than that of effluent from the no vegetation zone, and the temperature of the effluent from the vegetation zones are lower than that from the no vegetation zones. The submerged plants have special role in water quality improvement, and should be studied further.