Analyzing the evolution of insect TMED gene and the expression pattern of silkworm TMED gene / 生物工程学报

Transmembrane emp24 domain (TMED) gene is closely related to immune response, signal transduction, growth and disease development in mammals. However, only the Drosophila TMED gene has been reported on insects. We identified the TMED family genes of silkworm, Tribolium castaneum, tobacco moth and Italian bee from their genomes, and found that the TMED family gene composition patterns of one α-class, one β-class, one δ-class and several γ-classes arose in the common ancestor of pre-divergent Hymenoptera insects, while the composition of Drosophila TMED family members has evolved in a unique pattern. Insect TMED family γ-class genes have evolved rapidly, diverging into three separate subclasses, TMED6-like, TMED5-like and TMED3-like. The TMED5-like gene was lost in Hymenoptera, duplicated in the ancestors of Lepidoptera and duplicated in Drosophila. Insect TMED protein not only has typical structural characteristics of TMED, but also has obvious signal peptide. There are seven TMED genes in silkworm, distributed in six chromosomes. One of seven is single exon and others are multi-exons. The complete open reading frame (ORF) sequences of seven TMED genes of silkworm were cloned from larval tissues and registered in GenBank database. BmTMED1, BmTMED2 and BmTMED6 were expressed in all stages and tissues of the silkworm, and all genes were expressed in the 4th and 5th instar and silk gland of the silkworm. The present study revealed the composition pattern of TMED family members, their γ class differentiation and their evolutionary history, providing a basis for further studies on TMED genes in silkworm and other insects.

Tracking the spread of avian influenza in China: a model based on evolutionary genetics analysis and geographic visualization / 中华急诊医学杂志

ObjectiveTo explore the diverse natural and human factors affect the outbreak and spread of avian influenza. We integrated geographic visualization and evolutionary genetics technique to establish a method to track spread of avian influenza in China.MethodsThe sequence data of type A avian flu virus were provided by NCBI Nucleotide and Protein Databases.We transformed the original data to readable structures for Matlab using E-Utilities software.These MATLAB readable structures represented 8 genes of the virus,they are:RNA polymerase B2 (PB2),polymerase B1 (PB1),polymerase A (PA),hemagglutinin (HA),nucleoprotein (NP),ne(ur)al aminidase (NA),matrix (M1),and non-structural ( NS1 ) proteins.Based on these readable structures,we compared Ka/Ks ratio of different virus strains and identified the gene mutation patterns under different selection pressures.Then we selected the gene that exhibited the highest Ka/Ks ratio and performed a phylogenetic analysis by Jukes-Cantor algorithm.Google Earth layer tools were then used to integrate gene variation and geographic transmission information. Results When we compared these 8 virus genes,the NS1,HA and NA were found to exhibit high Ka/Ks ratio and could be seen to represent the transmission capacity of the virus.Among these,the HA gene has the highest Ka/Ks ratio.When we compare the amino acids encoded by the HA gene using clustering analysis,we found that the relationship between H5N1 avian influenza strains since 2003 in Asia made up an evolutionary tree.This evolutionary tree contained 30 nodes ( 14 branch nodes and 16 leaf nodes).All genes were classified into 4 major groups by the first 3 nodes. And these 4 groups exhibit clear geographic patterns in their spread.The impact of geographic factors on the outbreak of avian influenza in China can be ranked as:inland water bodies ( lakes,reservoirs)＞ major railway paths ＞ density of poultry. ConclusionsThe analysis on the dominant strains' gene mutations in China' s H5N1 found that the outbreaks of avian influenza correlate with avian migration and poultry transportation.