De novo assembly of a Chinese soybean genome

Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.

Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia

Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism.The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat changes.However,there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig pollinators.In fig syconia,there are also non-pollinator species.The non-pollinator species differ in their evolutionary and life histories from pollinators.We conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published genome.The pollinators colonized the figs approximately 66.9 million years ago,consistent with the origin of host figs.Compared with nonpollinators,many more genes in pollinators were subject to relaxed selection.Seven genes were absent in pollinators in response to environmental stress and immune activation.Pollinators had more streamlined gene repertoires in the innate immune system,chemosensory toolbox,and detoxification system.Our results provide genomic evidence for the differentiation between pollinators and nonpollinators.The data suggest that owing to the long-term adaptation to the fig,some genes related to functions no longer required are absent in pollinators.

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

While it is widely accepted that genetic diversity determines the potential of adaptation,the role that gene expression variation plays in adaptation remains poorly known.Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius.RNA-seq was conducted for 80 individuals of the species,with half planted in the energy crop domestication site and the other half planted in the control site near native habitats.A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data.The population structure and genetic diversity of M.lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms.Population expression（Ep） and expression diversity（Ed）were defined to measure the average level and the magnitude of variation of a gene expression in the population,respectively.It was found that expression diversity increased while genetic Resediversity decreased after the species was transplanted from the native habitats to the harsh domestication site,especially for genes involved in abiotic stress resistance,histone methylation,and biomass synthesis under water limitation.The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.