Assembly and RNA‐free annotation of highly heterozygous genomes: The case of the thick‐billed murre (Uria lomvia)

Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick‐billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray /sscape , soapdenovo 2 and platanus , in assembling the highly heterozygous genome of the thick‐billed murre. Our results show that platanus , an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick‐billed murre genome using a homology‐based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.     

Allelic imbalance metre (Allim), a new tool for measuring allele‐specific gene expression with RNA‐seq data

Estimating differences in gene expression among alleles is of high interest for many areas in biology and medicine. Here, we present a user‐friendly software tool, Allim, to estimate allele‐specific gene expression. Because mapping bias is a major problem for reliable estimates of allele‐specific gene expression using RNA‐seq, Allim combines two different strategies to account for the mapping biases. In order to reduce the mapping bias, Allim first generates a polymorphism‐aware reference genome that accounts for the sequence variation between the alleles. Then, a sequence‐specific simulation tool estimates the residual mapping bias. Statistical tests for allelic imbalance are provided that can be used with the bias corrected RNA‐seq data.     

A comparison of honeybee (Apis mellifera) queen,worker and drone larvae by RNA‐Seq

Honeybees (Apis mellifera) have haplodiploid sex determination: males develop from unfertilized eggs and females develop from fertilized ones. The differences in larval food also determine the development of females. Here we compared the total somatic gene expression profiles of 2-day and 4-day-old drone, queen and worker larvae by RNASeq. The results from a co-expression network analysis on all expressed genes showed that 2-day-old drone and worker larvae were closer in gene expression profiles than 2-day-old queen larvae. This indicated that for young larvae (2-day-old) environmental factors such as larval diet have a greater effect on gene expression profiles than ploidy or sex determination. Drones had the most distinct gene expression profiles at the 4-day larval stage, suggesting that haploidy, or sex dramatically affects the gene expression of honeybee larvae. Drone larvae showed fewer differences in gene expression profiles at the 2-day and 4-day time points than the worker and queen larval comparisons (598 against 1190 and 1181), suggesting a different pattern of gene expression regulation during the larval development of haploid males compared to diploid females. This study indicates that early in development the queen caste has the most distinct gene expression profile, perhaps reflecting the very rapid growth and morphological specialization of this caste compared to workers and drones. Later in development the haploid male drones have the most distinct gene expression profile, perhaps reflecting the influence of ploidy or sex determination on gene expression.     

RNA‐sequencing profiles hippocampal gene expression in a validated model of cancer‐induced depression

To investigate the pathophysiology of cancer‐induced depression (CID), we have recently developed a validated CID mouse model. Given that the efficacy of antidepressants in cancer patients is controversial, it remains unclear whether CID is a biologically distinct form of depression. We used RNA‐sequencing (RNA‐seq) to investigate differentially expressed genes (DEGs) in hippocampi of animals from our CID model relative a positive control model of depressive‐like behavior induced with chronic corticosterone (CORT). To validate RNA‐seq results, we performed quantitative real‐time RT‐PCR (qRT‐PCR) on a subset of DEGs. Enrichment analysis using DAVID was performed on DEGs to identify enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and biological process gene ontologies (GO:BP). qRT‐PCR results significantly predicted RNA‐seq results. RNA‐seq revealed that most DEGs identified in the CORT model overlapped with the CID model. Enrichment analyses identified KEGG pathways and GO:BP terms associated with ion homeostasis and neuronal communication for both the CORT and CID model. In addition, CID DEGs were enriched in pathways and terms relating to neuronal development, intracellular signaling, learning and memory. This study is the first to investigate CID at the mRNA level. We have shown that most hippocampal mRNA changes that are associated with a depressive‐like state are also associated with cancer. Several other changes occur at the mRNA level in cancer, suggesting that the CID model may represent a biologically distinct form of a depressive‐like state.     

Density‐dependent sex‐biased development of macroptery in a water strider

In wing‐polymorphic insects, wing morphs differ not only in dispersal capability but also in life history traits because of trade‐offs between flight capability and reproduction. When the fitness benefits and costs of producing wings differ between males and females, sex‐specific trade‐offs can result in sex differences in the frequency of long‐winged individuals. Furthermore, the social environment during development affects sex differences in wing development, but few empirical tests of this phenomenon have been performed to date. Here, I used the wing‐dimorphic water strider Tenagogerris euphrosyne to test how rearing density and sex ratio affect the sex‐specific development of long‐winged dispersing morphs (i.e., sex‐specific macroptery). I also used a full‐sib, split‐family breeding design to assess genetic effects on density‐dependent, sex‐specific macroptery. I reared water strider nymphs at either high or low densities and measured their wing development. I found that long‐winged morphs developed more frequently in males than in females when individuals were reared in a high‐density environment. However, the frequency of long‐winged morphs was not biased according to sex when individuals were reared in a low‐density environment. In addition, full‐sib males and females showed similar macroptery incidence rates at low nymphal density, whereas the macroptery incidence rates differed between full‐sib males and females at high nymphal density. Thus complex gene‐by‐environment‐by‐sex interactions may explain the density‐specific levels of sex bias in macroptery, although this interpretation should be treated with some caution. Overall, my study provides empirical evidence for density‐specific, sex‐biased wing development. My findings suggest that social factors as well as abiotic factors can be important in determining sex‐biased wing development in insects.     

Role of male‐biased dispersal in inbreeding avoidance in the grey‐sided vole (Myodes rufocanus)

Effects of male‐biased dispersal on inbreeding avoidance were investigated in a semi‐natural population of Myodes (formerly Clethrionomys) rufocanus using a large outdoor enclosure (3 ha). Parentage of 918 voles weaned from 215 litters and relatedness of mates were analysed using microsatellite loci, and dispersal distances were obtained from mark–recapture live‐trapping data. Natal and breeding male‐biased dispersal was observed. There remained, however, chances that incestuous mating could occur, because not all males dispersed from their natal site, and 51 matings occurred between relatives (relatedness r > 0). The number of weaned juveniles from inbred litters was significantly smaller than that from non‐inbred litters. Fourteen incestuous matings occurred between close relatives (r ≥ 0.25), most of which were those between non‐littermate maternal half siblings (four cases) and those between paternal half siblings (seven cases). When comparing the observed frequencies to the expected ones generated by combining every oestrous female with a male randomly chosen from her surroundings, the observed values for inbreeding of r ≥ 0.25 were significantly smaller than the expectations, while no difference was observed for inbreeding of 0 < r < 0.25. These results suggest that male‐biased dispersal is partly effective to avoid incestuous mating, but it does not provide complete separation of male and female close relatives. Additional mechanisms such as kin discrimination based on familiarity may work in inbreeding avoidance of the vole.     

Evaluation of the Stag3 gene and the synaptonemal complex in a rat model (as/as) for male infertility

Affected males (as/as) from the mutant TT rat strain are sterile due to spermatogenesis impairment with meiotic arrest at the pachytene stage. The as locus is on rat chromosome 12, in a region that shows conserved synteny to cM 74-94 on mouse chromosome 5. Stag3, a new member of the stromalin protein family, is expressed specifically in testis and associates to the synaptonemal complex. Mouse Stag3 gene has been assigned to cM 78 on chromosome 5. In this study, we have characterized the rat Stag3 gene and examined it as a candidate for male infertility in as/as rats. The rat Stag3 cDNA is 4181 nucleotides long, contains a highly polymorphic hexanucleotide repeat in the coding region, and encodes a 1256 amino acid protein with 93 and 77% sequence identity to mouse and human Stag3 proteins, respectively. No mutations or differences in size or abundance of Stag3 mRNA were detected between as/as and control rats, suggesting that Stag3 is not responsible for the aspermic phenotype. In addition, immunohistochemistry with antibodies against SCP1 and SPC3 proteins suggest that the synaptonemal complex structures are not primarily affected in these rats.     

Induction of host‐plant preference in Brontispa longissima (Gestro) (Coleoptera: Chrysomelidae)

The coconut hispine beetle, Brontispa longissima, is a serious invasive pest of coconut palm (Cocos nucifera) in Southeast Asia and the Pacific region. Recently, however, it has been reported that on Ishigaki Island, Japan, where C. nucifera is rare, the endemic palm Satakentia liukiuensis serves as a regular host. To explore this phenomenon, we examined the preferences of the beetle for the two palm hosts by choice tests and measurements of feeding amount using four different groups: naïve adults obtained from a colony reared on C. nucifera (NC); naïve adults from a colony reared on S. liukiuensis (NS); wild adults collected on C. nucifera on Ishigaki Island (WC); and wild adults collected on S. liukiuensis on Ishigaki Island (WS). Both NC and NS consumed significantly more C. nucifera leaves than S. liukiuensis leaves and were observed more often on the leaves of C. nucifera. These results suggest that B. longissima has an innate preference for C. nucifera. In contrast, field‐collected adults (WC, WS) initially showed preferences for the species on which they were collected, but after exposure to the other host plant for 2 weeks, their preferences for that host increased. These results suggest that the feeding experience of B. longissima adults affected their subsequent host preferences. This flexible host preference may have facilitated the beetle’s successful establishment in novel Japanese habitats where the original host plant was rare.     

Strongly female‐biased sex allocation in a trivoltine population of Trypoxylon (Trypargilum) opacum Brèthes (Hymenoptera,Crabronidae)

Buschini, M.L.T. and Bergamaschi, A.C.B. 2009. Strongly female‐biased sex allocation in a trivoltine population of Trypoxylon (Trypargilum) opacum Brèthes (Hymenoptera, Crabronidae). —Acta Zoologica (Stockholm) 91 : 433–439. This study was carried in southern Brazil from December 2001 to December 2004. The aim of this paper is to provide additional information on the life‐history and sex allocation of this little known species. This wasp’s species has two alternative life histories: either they pupated immediately and emerged as adults later in the same season (direct development) or they entered diapause, overwintering and pupating the following spring (delayed development). The numerical sex ratio of overwintering and of direct developing wasps were strongly female biased in 2002, 2003 and 2004.     

Genome‐wide association study reveals novel genes for the ear size in sheep (Ovis aries)

Variations in ear size can be observed in livestock such as sheep; however, the genetic basis of variable ear size in sheep is still poorly understood. To investigate causative genes associated with ear size in sheep, a genome‐wide association study was performed in 115 adult Duolang sheep with different‐sized floppy ears using the Ovine Infinium HD BeadChip. We found 38 significant SNPs at the genome‐wide or chromosome‐wise 5% significance level after Bonferroni correction. The most significant association (P = 1.61 × 10^?6) was found at SNP rs402740419, located in the DCC gene, which plays a critical role in ear development. Also, we observed two additional significant SNPs, rs407891215 in PTPRD and rs407769095 in SOX5, both of which are functionally associated with ear developmental processes. Our results are useful for future sheep breeding and provide insights into the genetic basis of ear size development in sheep and other livestock.     

Mating rates and the prevalence of male‐killing Spiroplasma in Harmonia axyridis (Coleoptera: Coccinellidae)

Maternally inherited bacteria that kill male but not female hosts during embryogenesis have been widely reported in invertebrates. Harmonia axyridis is one of the species infected by male‐killing Spiroplasma. The presence of male‐killers in host populations can lead to the occurrence of extremely female‐biased sex ratios. Furthermore, infected females may have fewer chances to mate if males can discriminate between infected and uninfected females and prefer the latter. Although there have been many investigations of male‐killer infection rates in H. axyridis, little is known about the influence of host mating on male‐killer infection dynamics. We investigated copulation rates and changes in infection frequency in a wild population of H. axyridis in western Japan. Almost all infected females collected each year laid fertilized eggs and had therefore mated. Mean infection rates of females collected each year were 13% in 2003, 15% in 2012 and 23% in 2013. Statistical analysis showed that neither the copulation rate nor the infection rate differed significantly among years. These results suggest that the infection rate of H. axyridis with male‐killing Spiroplasma is kept approximately constant and that there is no difference in the chance of mating with infected and uninfected females.     

Sex determination in cucumber (Cucumis sativus) as a model system for molecular biology

Floral biology and sex determination are reviewed in cucumber, one of the best studied monoecious plant systems. Sexual differentiation is controlled by genotypic and environmental factors. Sex conversion has been achieved by a variety of chemical treatments, some of which being extensively used for commercial purposes. Sex expression can be shifted in either direction: femaleness is promoted by ethylene, auxines and ethylene releasing compounds, while maleness is induced by gibberellins and chemicals counteracting ethylene action. Agrobacterium transformation affects, albeit rather nonspecifically, sex expression. An important collection of sex and floral mutants has been developed. The expression of sex genes has been shown to be under the control of modifier genes or the environment. Cloning strategies can take profit of the fact that sex conversion can be modulated alone or in combination by genetical, chemical and/or environmental parameters.