Genetic polymorphism of mitochondrial DNA HVS-I and HVS-II of Chinese Tu ethnic minority group

We analyzed the two hypervariable segments HVS-I and HVS-II of 108 Chinese Tu ethnic minority group samples for forensic and population genetics purposes, Comparing with Anderson sequence, 79 polymorphic loci in HVS-I and 40 in HVS-II were found in Chinese Tu ethnic minority group mtDNA sequences, and 90 and 64 haplotypes were then defined. Haplotype diversity and the mean pairwise differences were 0.9903±0.0013 and 5.7785 in HVS-I, and 0.9777±0.0013 and 3.5819 in HVS-II, respectively. By analyzing the hypervariable domain from nucleotide 1,6180 to 1,6193 in HVS-I, we defined some new types of sequence variations. We also compared the relationship between Tu population and other populations using mtDNA HVS-I sequences. According to Rst genetic distances, the phylogenetic tree showed that the Tu population, the Xi＇an Han population, the Chinese Korean, and the Mongol ethnic group were in a clade. This indicated a close genetic relationship between them. There were far relations between the Tu population and other Chinese southern Han populations, Siberian, European, African, and other foreign populations. The results suggest that Tu population has a multi-origin and has also merged with other local populations.

A pangenomic study of Bacillus thuringiensis

Bacillus thuringiensis（B.thuringiensis） is a soil-dwelling Gram-positive bacterium and its plasmid-encoded toxins（Cry） are commonly used as biological alternatives to pesticides.In a pangenomic study,we sequenced seven B.thuringiensis isolates in both high coverage and base-quality using the next-generation sequencing platform.The B.thuringiensis pangenome was extrapolated to have 4196 core genes and an asymptotic value of 558 unique genes when a new genome is added.Compared to the pangenomes of its closely related species of the same genus,B.thuringiensis pangenome shows an open characteristic,similar to B.cereus but not to B.anthracis;the latter has a closed pangenome. We also found extensive divergence among the seven B.thuringiensis genome assemblies,which harbor ample repeats and single nucleotide polymorphisms（SNPs）.The identities among orthologous genes are greater than 84.5%and the hotspots for the genome variations were discovered in genomic regions of 2.3-2.8 Mb and 5.0-5.6 Mb.We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed,are very useful for pangenomic studies.

Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

The red palm weevil （RPW）, Rhynchophorus ferrugineus （Coleoptera： Cur- culionidae）, is an invasive, concealed and destructive tissue borer, and it becomes a lethal pest of the palm family of plants and has been reported to attack 20 palm species around the globe. Here we report a systematic transcriptomic study on embryogenesis of RPW, where we analyze the transcriptomes across five developmental stages of RPW embryogenesis, involving four embryonic stages （El, E2, E3 and E4） and one larval stage （L1）. Using the RNA-seq and next-generation platforms, we generated 80 to 91 million reads for each library and assemble 22 532 genes that are expressed at different embryonic stages. Among the total transcripts from the five embryonic development stages, we found that 30.45 % are differentially expressed, 10.10 % show stage-specificity and even a larger fraction, 62.88 %, exhibit constitutive expression in all the stages. We also analyzes the expression dynamics of several conserved signaling pathways （such as Hedgehog, JAK-STAT, Notch, TGF-β, Ras/MAPK and Writ）, as well as key developmental genes, including those related to apoptosis, axis formation, Hox complex, neurogenesis and segmentation. The datasets provide an essential resource for gene annotation and RPW functional genomics, including studies by using tools and concepts from multiple disciplines, such as development, physiology, biochemistry, molecular biology and genetics.