Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes, the A. mellifera genome has high A+T and CpG contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, RNA interference and DNA methylation genes, among others. Furthermore, A. mellifera has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen utilization, consistent with its ecology and social organization. Compared to Drosophila, genes in early developmental pathways differ in Apis, whereas similarities exist for functions that differ markedly, such as sex determination, brain function and behaviour. Population genetics suggests a novel African origin for the species A. mellifera and insights into whether Africanized bees spread throughout the New World via hybridization or displacement.

DNA methylation systems are well characterized in vertebrates, but methylation in Drosophila melanogaster and other invertebrates remains controversial. Using the recently sequenced honey bee genome, we present a bioinformatic, molecular, and biochemical characterization of a functional DNA methylation system in an insect. We report on catalytically active orthologs of the vertebrate DNA methyltransferases Dnmt1 and Dnmt3a and b, two isoforms that contain a methyl-DNA binding domain, genomic 5-methyl-deoxycytosine, and CpG-methylated genes. The honey bee provides an opportunity to study the roles of methylation in social contexts.

Domestic ducks are natural reservoirs of avian influenza viruses and serve as reassortant hosts for new virus subtypes. We isolated 2 novel influenza A(H5N8) viruses from domestic ducks in eastern China, sequenced their genomes, and tested their pathogenicity in chickens and mice. Circulation of these viruses may pose health risks for humans.

The objectives of this study were to examine antioxidant enzyme responses to drought stress and rewatering at both enzymatic activity and transcript levels and to determine the major antioxidant processes associated with drought tolerance and post-drought recovery for a perennial grass species, kentucky bluegrass (Poa pratensis). Antioxidant enzyme responses to drought and rewatering in a drought-tolerant cultivar (Midnight) and a drought-sensitive cultivar (Brilliant) were compared in a growth chamber. Plants were exposed to 22 days of drought stress for ‘Midnight’ and 18 days for ‘Brilliant’ before rewatering to allow the leaf relative water content (RWC) of both cultivars to drop to the same level. ‘Midnight’ exhibited higher photochemical efficiency (Fv/Fm) and lower electrolyte leakage compared with ‘Brilliant’ when at the same water deficit status (26% to 28% RWC). After 6 days of rewatering, all physiological parameters returned to the control level for ‘Midnight’, but only Fv/Fm fully recovered for ‘Brilliant’. The transcript level of cytosolic copper/zinc superoxide dismutase (cyt Cu/Zn SOD) and ascorbate peroxidase (APX) was significantly higher in ‘Midnight’ than in ‘Brilliant’ when exposed to the same level of water deficit (26% to 28% RWC), suggesting that SOD and APX could be involved in scavenging oxidative stress-induced reactive oxygen species in kentucky bluegrass through changes in the level of gene expression. Significantly higher activities of APX, monodehydroascorbate reductase, glutathione reductase, and dehydroascorbate reductase as well as lower lipid peroxidation levels were observed in ‘Midnight’ versus ‘Brilliant’ when exposed to drought. However, the activities of SOD, catalase (CAT), and guaiacol peroxidase (POD) did not differ between the two cultivars. After 6 days of rewatering, ‘Midnight’ displayed significantly higher activity levels of CAT, POD, and APX compared with ‘Brilliant’. The enzyme activity results indicate that enzymes involved in the ascorbate–glutathine cycle may play important roles in antioxidant protection to drought damage, whereas CAT, POD, and APX could be associated with better post-drought recovery in kentucky bluegrass.

BackgroundRed clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on red clover.ResultsIn this study, the red clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2194 novel isoforms from novel genes were identified. A total of 5492 alternative splicing events was identified and the majority of alter spliced events in red clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8719 including 186,517 transcripts have at least one poly(A) site. Furthermore, we identified 4333 long non-coding RNAs and 3762 fusion transcripts.ConclusionsWe analyzed full-length transcriptome of red clover with PacBio SMRT. Those new findings provided important information for improving red clover draft genome annotation and fully characterization of red clover transcriptome.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1534-8) contains supplementary material, which is available to authorized users.