Conserved profiles of digestion by double restriction endonucleases in insect genomes facilitate the design of dd RAD

Double-digested Restriction Site Associated DNA Sequencing（ddRAD） through next-generation sequencing（NGS） generates large numbers of loci for characterizing genomewide variation among multiple samples using next-generation sequencing. Different combinations of restriction endonucleases（REs） may produce varying size distributions of digested fragments, which affect the number of genotyped loci. Understanding digestion profiles across different species will help in selecting REs for digestion in a particular organism. In this study, we use of genome sequences to compare the in silico digestion profile of 26 combinations of REs in 131 insect species with two simulation programs. The number of digested fragments in the 300-450 bp range increases linearly with the size of the genome. Different species and insect orders showed similar profiles when digested by different combinations of REs in silico, indicating the conservation of digestion by double enzymes in insect genomes. Combinations with Nla III or TaqαI usually produced higher number of fragments in the range 300-450 bp, while combinations with EcoRI or MluCI produced fewer fragments. The proportion of fragments with the same overhangs at the two ends of digested DNA was higher than those with different overhangs. The two four-base enzyme pairs produced more fragments in the 300-450 bp range than pairs of four-base ＋ six-base enzymes. Experimental digestion of three species from Hymenoptera, Lepidoptera and Thysanoptera showed profiles congruent with in silico expectations. Our results shed light on understanding the digestion profiles of insect genomes and provide guidance on selecting REs for ddRAD projects.

Decoding transcriptional regulation via a human gene expression predictor

Transcription factors(TFs)regulate cellular activities by controlling gene expression,but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking.We construct a universal human gene expression predictor named EXPLICIT-Human and utilize it to decode transcriptional regulation.Using the expression of 1613 TFs,the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and conditions.The broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across tissues.Significant interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development,immunity,metabolism,and stress response.A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages,and a portion of these TFs are conserved between humans and mice.The results demonstrate that our method is capable of delineating the TFs responsible for fate determination.Compared to other existing tools,EXPLICIT-Human shows a better performance in recovering the correct TF regulators.

The consistency between Na content distribution at the subsurface and the lake body’s movement in Lop Nur

Historically,Lop Nur was a large and famous salt lake that acted as an important geographic position along the ancient‘Silk Road’,and was associated with the surrounding old civilizations,such as Loulan and Haitou.However,it dried up before 1972.It shows a clear‘Ear’feature on synthetic aperture radar(SAR)images.The objective of this paper is to interpret Lop Nur’s environmental evolution during its drying-up process based on an analysis of its sodium sedimentary feature.The genetic algorithm-partial least squares approach is introduced as a modeling method to retrieve the subsurface sodium content from polarimetric parameters obtained by Cloude decomposition.As a result,the R2 and root-mean-square error can reach 0.7 and 9.1 g/kg.It is suggested that the subsurface salt content was the primary reason for the bright-grey strips textures on SAR images.Furthermore,our results show that the sodium content along the same strip changed,with its distribution exhibiting consistency with the lake body’s movement driven by the strong wind.In future,high-precision topographical data will be considered,and should be helpful in the analysis of lake body movement.The method of this paper can also be applied in other similar dried salt lakes.