Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica

Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world's most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica.

Color as an Interspecific Badge of Status: A Comparative Test

AbstractAnimals as diverse as cephalopods, insects, fish, and mammals signal social dominance to conspecifics to avoid costly fights. Even though between-species fights may be equally costly, the extent to which dominance signals are used between species is unknown. Here, we test the hypothesis that differences in color are associated with dominance between closely related species that aggressively interact over resources, examining between-species variation in colors that are used in within-species badges of status (black, white, and carotenoid coloration) in a comparative analysis of diverse species of birds. We found that dominant species have more black, on average, than subordinate species, particularly in regions important for aggressive signaling (face, throat, and bill). Furthermore, dominant species were more likely to have more black in comparisons in which the dominant species was similar in size or smaller than the subordinate, suggesting that black may be a more important signal when other signals of dominance (size) are missing. Carotenoid colors (i.e., red, pink, orange, and yellow) were not generally associated with dominance but may signal dominance in some taxonomic groups. White may have opposing functions: white was associated with dominance in species in which black was also associated with dominance but was associated with subordinance in species in which carotenoid-based dominance signals may be used. Overall, these results provide new evidence that colors may function broadly as signals of dominance among competing species. Such signals could help to mediate aggressive interactions among species, thereby reducing some costs of co-occurrence and facilitating coexistence in nature.

Spatial Overlap and Habitat Selection of Corvid Species in European Cities

Understanding habitat and spatial overlap in sympatric species of urban areas would aid in predicting species and community modifications in response to global change. Habitat overlap has been widely investigated for specialist species but neglected for generalists living in urban settings. Many corvid species are generalists and are adapted to urban areas. This work aimed to determine the urban habitat requirements and spatial overlap of five corvid species in sixteen European cities during the breeding season. All five studied corvid species had high overlap in their habitat selection while still having particular tendencies. We found three species, the Carrion/Hooded Crow, Rook, and Eurasian Magpie, selected open habitats. The Western Jackdaw avoided areas with bare soil cover, and the Eurasian Jay chose more forested areas. The species with similar habitat selection also had congruent spatial distributions. Our results indicate that although the corvids had some tendencies regarding habitat selection, as generalists, they still tolerated a wide range of urban habitats, which resulted in high overlap in their habitat niches and spatial distributions.

Evolution is driven by natural autoencoding: reframing species, interaction codes, cooperation and sexual reproduction

The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process survival of the fitted. Here, we reason that survival of the fitted results from a natural computational process we term natural autoencoding. Natural autoencoding works by retaining repeating biological interactions while non-repeatable interactions disappear. (i) We define a species by its species interaction code, which consists of a compact description of the repeating interactions of species organisms with their external and internal environments. Species interaction codes are descriptions recorded in the biological infrastructure that enables repeating interactions. Encoding and decoding are interwoven. (ii) Evolution proceeds by natural autoencoding of sustained changes in species interaction codes. DNA is only one element in natural autoencoding. (iii) Natural autoencoding accounts for the paradox of genome randomization in sexual reproduction-recombined genomes are analogous to the diversified inputs required for artificial autoencoding. The increase in entropy generated by genome randomization compensates for the decrease in entropy generated by organized life. (iv) Natural autoencoding and artificial autoencoding algorithms manifest defined similarities and differences. Recognition of the importance of fittedness could well serve the future of a humanly livable biosphere.

Divergence in interspecific and intersubspecific gene expression between two closely related horseshoe bats (Rhinolophus)

Closely related species have been used as representative systems to investigate the genetic mechanisms involved in the early stages of species differentiation. Previous studies have indicated that variation in gene expression might be a sensitive indicator of initial species divergence, although the role of expression divergence, and especially that associated with phenotypic variation remained relatively undefined. For three organs (cochlea, brain, and liver) from two closely related bat species (Rhinolophus siamensis and R. episcopus), the interspecific and intersubspecific gene expression profiles were compared using transcriptomics in this study. Striking organ specificity of expression was observed, and expression profiles exhibited similarities between cochlea and brain tissues. Numerous differentially expressed genes (DEGs) were identified for each organ in the interspecific comparison (cochlea/brain/liver: 1,069/647/692) and intersubspecific comparison (608/528/368). Functional enrichment analysis indicated vital variation in expression related to the immune system, ion activities, neuronal function, and multisensory system regulation in both comparisons. DEGs relevant to the variation in echolocation calls (RF) were found, and some of them were involved in the pivotal patterns of expression variation. The regulation of immune, ion channel, neural activity, and sophisticated sensory functions at the expression level might be key mechanisms in the early species divergence of bats, and the expression variation related to acoustical signal could have played a crucial part. This study expands our knowledge of gene expression and patterns of variation for three key organs to echolocation at both the interspecific and intersubspecific levels. Further, the framework described here provides insight into the genetic basis of phenotypic variation during the incipient stage of species differentiation.

Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs

In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.

Gene expression and genetic divergence in oak species highlight adaptive genes to soil water constraints

Drought and waterlogging impede tree growth and may even lead to tree death. Oaks, an emblematic group of tree species, have evolved a range of adaptations to cope with these constraints. The two most widely distributed European species, pedunculate (PO; Quercus robur L.) and sessile oak (SO; Quercus petraea Matt. Lieb), have overlapping ranges, but their respective distribution are highly constrained by local soil conditions. These contrasting ecological preferences between two closely related and frequently hybridizing species constitute a powerful model to explore the functional bases of the adaptive responses in oak. We exposed oak seedlings to waterlogging and drought, conditions typically encountered by the two species in their respective habitats, and studied changes in gene expression in roots using RNA-seq. We identified genes that change in expression between treatments differentially depending on species. These "species × environment"-responsive genes revealed adaptive molecular strategies involving adventitious and lateral root formation, aerenchyma formation in PO, and osmoregulation and ABA regulation in SO. With this experimental design, we also identified genes with different expression between species independently of water conditions imposed. Surprisingly, this category included genes with functions consistent with a role in intrinsic reproductive barriers. Finally, we compared our findings with those for a genome scan of species divergence and found that the expressional candidate genes included numerous highly differentiated genetic markers between the two species. By combining transcriptomic analysis, gene annotation, pathway analyses, as well as genome scan for genetic differentiation among species, we were able to highlight loci likely involved in adaptation of the two species to their respective ecological niches.

Salinity-induced transcriptome profiles in marine and freshwater threespine stickleback after an abrupt 6-hour exposure

Saltwater and freshwater environments have opposing physiological challenges, yet, there are fish species that are able to enter both habitats during short time spans, and as individuals they must therefore adjust quickly to osmoregulatory contrasts. In this study, we conducted an experiment to test for plastic responses to abrupt salinity changes in two populations of threespine stickleback, Gasterosteus aculeatus, representing two ecotypes (freshwater and ancestral saltwater). We exposed both ecotypes to abrupt native (control treatment) and non‐native salinities (0‰ and 30‰) and sampled gill tissue for transcriptomic analyses after 6 h of exposure. To investigate genomic responses to salinity, we analyzed four different comparisons; one for each ecotype (in their control and exposure salinity; (1) and (2), one between ecotypes in their control salinity (3), and the fourth comparison included all transcripts identified in (3) that did not show any expressional changes within ecotype in either the control or the exposed salinity (4)). Abrupt salinity transfer affected the expression of 10 and 1530 transcripts for the saltwater and freshwater ecotype, respectively, and 1314 were differentially expressed between the controls, including 502 that were not affected by salinity within ecotype (fixed expression). In total, these results indicate that factors other than genomic expressional plasticity are important for osmoregulation in stickleback, due to the need for opposite physiological pathways to survive the abrupt change in salinity.

A brain atlas of the carrion crow (Corvus corone)

Corvidae, passerine songbirds such as jays, crows, and ravens known as corvids, have become model systems for the study of avian cognition. The superior cognitive capabilities of corvids mainly emerge from a disproportionally large telencephalon found in these species. However, a systematic mapping of the neuroanatomy of the corvid brain, and the telencephalon in particular, is lacking so far. Here, we present a brain atlas of the carrion crow, Corvus corone, with special emphasis on the telencephalic pallium. We applied four staining techniques to brain slices (Nissl, myelin, combination of Nissl and myelin, and tyrosine hydroxylase targeting catecholaminergic neurons). This allowed us to identify brain nuclei throughout the brain and delineate the known pallial subdivisions termed hyperpallium, entopallium, mesopallium, nidopallium, arcopallium, and hippocampal complex. The extent of these subdivisions and brain nuclei are described according to stereotaxic coordinates. In addition, 3D depictions of pallial regions were reconstructed from these slices. While the overall organization of the carrion crow's brain matches other songbird brains, the relative proportions and expansions of associative pallial areas differ considerably in agreement with enhanced cognitive skills found in corvids. The presented global organization of the crow brain in stereotaxic coordinates will help to guide future neurobiological studies in corvids.

Correlates of hybridization in plants

Hybridization is a biological phenomenon increasingly recognized as an important evolutionary process in both plants and animals, as it is linked to speciation, radiation, extinction, range expansion and invasion, and allows for increased trait diversity in agricultural and horticultural systems. Estimates of hybridization frequency vary across taxonomic groups, but causes of this variation are unknown. Here, we ask on a global scale whether hybridization is linked to any of 11 traits related to plant life history, reproduction, genetic predisposition, and environment or opportunity. Given that hybridization is not evenly distributed across the plant tree of life, we use phylogenetic generalized least squares regression models and phylogenetic path analysis to detect statistical associations between hybridization and plant traits at both the family and genus levels. We find that perenniality and woodiness are each weakly associated with an increased frequency of hybridization in univariate analyses, but path analysis suggests that the direct linkage is between perenniality and increased hybridization (with woodiness having only an indirect relationship with hybridization via perenniality). Weak associations between higher rates of hybridization and higher outcrossing rates, abiotic pollination syndromes, vegetative reproductive modes, larger genomes, and less variable genome sizes are detectable in some cases but not others. We argue that correlational evidence at the global scale, such as that presented here, provides a robust framework for forming hypotheses to examine and test drivers of hybridization at a more mechanistic level.

Hybridism between Cyanocorax chrysops and Cyanocorax cyanopogon (Aves: Corvidae) in Brazil

Cyanocorax chrysops(Vieillot, 1818) andCyanocorax cyanopogon(Wied, 1821) are widespread jays. They are considered sister species according to recent molecular phylogenies. When analyzing museum specimens of both species, we found two individuals with intermediate plumage characteristics. They were collected near the range limits of both species, and we classified them as hybrids. Based on the sites where these specimens were found, we discuss the possible factors leading the interbreeding and compare our findings with information available in the literature. This is the first documented case of natural hybridization in jays in Brazil and the second case involving sister species within the New World jays.

Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F1 hybrid

Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.

Phylogeography and hybridization of corvid birds in the Palearctic Region

Natural hybridization increases a lot phenotypic and genetic diversity and shapes intra-species patterns, which is a subject of phylogeography. We studied mitochondrial and complete genome variation in the bird family Corvidae, genera Corvus, Pica, Cyanopica, Perisoreus and Nucifraga. In the classic case of natural hybridization between carrion and hooded crows in Siberia, we found no decreased fitness of hybrids, but instead positive assortative mating which should restrict hybrid zone width. Several genetic markers were unable to discriminate between pure carrion and hooded crows. Mitochondrial DNA sequences revealed no difference between carrion and hooded crows, but instead two diverged haplogroups within the eastern part of the distribution range of the carrion crow. NGS resulted in a clear pattern of diversification of pure forms and hybrids (by using SNPs), and showed genomic regions of increased variability, the so-called “speciation islands”. Comparing European and Siberian crow hybrid zones, differences in genome regions bearing genes of melanogenesis supposedly under divergent selection were found. Comparative phylogeographic analysis of 10 widely distributed Palearctic species revealed two kinds of patterns: one with a division into two haplogroups, western and eastern, and another one without such a division. These two phylogeographic patterns might be explained by different habitat preferences: mainly open fields for the first group and forests for the second one. One glacial refuge was assigned to the latter group, while west-east group species might have survived in several refuges. One of such species, the Eurasian magpie (Pica pica) has a gap in its range in Transbaikalia, which is currently shrinking before our eyes. The two subspecies divided by this gap differ in phenotype, mtDNA and vocalization. In their young contact zone, some hybridization occurs with small introgression limited by certain post-zygotic isolation.

Differences in Effective Ploidy Drive Genome-Wide Endosperm Expression Polarization and Seed Failure in Wild Tomato Hybrids

Parental imbalances in the endosperm leading to impaired development and eventual hybrid seed failure are common causes of postzygotic isolation in flowering plants. Endosperm sensitivity to parental dosage is reflected by canonical phenotypes of "parental excess" in reciprocal interploid crosses. Moreover, parental-excess traits are also evident in many homoploid interspecific crosses, potentially reflecting among-lineage variation in "effective ploidy" driven by endosperm properties. However, the genetic basis of effective ploidy is unknown and genome-wide expression perturbations in parental-excess endosperms from homoploid crosses have yet to be reported. The tomato clade (Solanum section Lycopersicon), encompassing closely related diploids with partial-to-complete hybrid seed failure, provides outstanding opportunities to study these issues. Here, we compared replicated endosperm transcriptomes from six crosses within and among three wild tomato lineages. Strikingly, strongly inviable hybrid crosses displayed conspicuous, asymmetric expression perturbations that mirror previously characterized parental-excess phenotypes. Solanum peruvianum, the species inferred to have evolved higher effective ploidy than the other two, drove expression landscape polarization between maternal and paternal roles. This global expression divergence was mirrored in functionally important gene families such as MADS-box transcription factors and E3 ubiquitin ligases, and revealed differences in cell cycle tuning that match phenotypic differences in developing endosperm and mature seed size between reciprocal crosses. Our work starts to uncover the complex interactions between expression divergence, parental conflict, and hybrid seed failure that likely contributed to plant diversity.

Genetic and Molecular Basis of Feather Diversity in Birds

Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.

Differential gene expression in the evolution of sex pheromone communication in New Zealand's endemic leafroller moths of the genera Ctenopseustis and Planotortrix

Background

Sex pheromone communication in moths has attracted the attention of evolutionary biologists due to the vast array of pheromone compounds used, addressing questions of how this diversity arose and how male reception has evolved in step with the female signal. Here we examine the role of changing gene expression in the evolution of mate recognition systems in leafroller moths, particularly focusing on genes involved in the biosynthetic pathways of sex pheromones in female pheromone glands and the peripheral reception repertoire in the antennae of males. From tissue-specific transcriptomes we mined and compared a database of genes expressed in the pheromone glands and antennae of males and females of four closely related species of leafroller moths endemic to New Zealand, Ctenopseutis herana and C. obliquana, and Planotortrix excessana and P. octo. The peculiarity of this group, compared to other Lepidoptera, is the use of (Z)-5-tetradecenyl acetate, (Z)-7-tetradecenyl acetate, and (Z)-8-tetradecenyl acetate as sex pheromone components.

Results

We identify orthologues of candidate genes from the pheromone biosynthesis pathway, degradation and transport, as well as genes of the periphery olfactory repertoire, including large families of binding proteins, receptors and odorant degrading enzymes. The production of distinct pheromone blends in the sibling species is associated with the differential expression of two desaturase genes, deast5 and desat7, in the pheromone glands. In male antennae, three odorant receptors, OR74, OR76a and OR30 are over-expressed, but their expression could not be clearly associated with the detection of species-specific pheromones components. In addition these species contain duplications of all three pheromone binding proteins (PBPs) that are also differentially expressed among species.

Conclusions

While in females differences in the expression of desaturases may be sufficient to explain pheromone blend differences among these New Zealand leafroller species, in males differential expression of several genes, including pheromone binding proteins, may underpin differences in the response by males to changing pheromone components among the species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4451-1) contains supplementary material, which is available to authorized users.

Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula)

BACKGROUND

In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed.

METHODS

Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R.

RESULTS

Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found.

DISCUSSION

Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype.

Insight into cordycepin biosynthesis of Cordyceps militaris: Comparison between a liquid surface culture and a submerged culture through transcriptomic analysis

Cordyceps militaris produces cordycepin, which is known to be a bioactive compound. Currently, cordycepin hyperproduction of C. militaris was carried out in a liquid surface culture because of its low productivity in a submerged culture, however the reason was not known. In this study, 4.92 g/L of cordycepin was produced at the 15^th day of C. militaris NBRC 103752 liquid surface culture, but only 1 mg/L was produced in the submerged culture. RNA-Seq was used to clarify the gene expression profiles of the cordycepin biosynthetic pathways of the submerged culture and the liquid surface culture. From this analysis, 1036 genes were shown to be upregulated and 557 genes were downregulated in the liquid surface culture compared with the submerged culture. Specifically, adenylosuccinate synthetase and phosphoribosylaminoimidazole-succinocarboxamide (SAICAR) synthase in purine nucleotide metabolism were significantly upregulated in the liquid surface culture. Thick mycelia formation in the liquid surface culture was found to induce the expression of hypoxia-related genes (GABA shunt, glutamate synthetase precursor, and succinate-semialdehyde dehydrogenase). Cytochrome P450 oxidoreductases containing heme were also found to be significantly enriched, suggesting that a hypoxic condition might be created in the liquid surface culture. These results suggest that hypoxic conditions are more suitable for cordycepin production in the liquid surface culture compared with the submerged culture. Our analysis paves the way for unraveling the cordycepin biosynthesis pathway and for improving cordycepin production in C. militaris.

Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops

The use of transcriptome data in the study of the population genetics of a species can capture faint signals of both genetic variation and expression variation and can provide a broad picture of a species' genomic response to environmental conditions. In this study, we characterized the genetic and expression diversity of Miscanthus lutarioriparius by comparing more than 16,225 transcripts obtained from 78 individuals, belonging to 10 populations distributed across the species' entire geographic range. We only observed a low level of nucleotide diversity (π = 0.000434) among the transcriptome data of these populations, which is consistent with highly conserved sequences of functional elements and protein-coding genes captured with this method. Tests of population divergence using the transcriptome data were consistent with previous microsatellite data but proved to be more sensitive, particularly if gene expression variation was considered as well. For example, the analysis of expression data showed that genes involved in photosynthetic processes and responses to temperature or reactive oxygen species stimuli were significantly enriched in certain populations. This differential gene expression was primarily observed among populations and not within populations. Interestingly, nucleotide diversity was significantly negatively correlated with expression diversity within populations, while this correlation was positive among populations. This suggests that genetic and expression variation play separate roles in adaptation and population persistence. Combining analyses of genetic and gene expression variation represents a promising approach for studying the population genetics of wild species and may uncover both adaptive and nonadaptive processes.

Do changes in gene expression contribute to sexual isolation and reinforcement in the house mouse?

Expression divergence, rather than sequence divergence, has been shown to be important in speciation, particularly in the early stages of divergence of traits involved in reproductive isolation. In the two European subspecies of house mice, Mus musculus musculus and Mus musculus domesticus, earlier studies have demonstrated olfactory-based assortative mate preference in populations close to their hybrid zone. It has been suggested that this behaviour evolved following the recent secondary contact between the two taxa (~3,000 years ago) in response to selection against hybridization. To test for a role of changes in gene expression in the observed behavioural shift, we conducted a RNA sequencing experiment on mouse vomeronasal organs. Key candidate genes for pheromone-based subspecies recognition, the vomeronasal receptors, are expressed in these organs. Overall patterns of gene expression varied significantly between samples from the two subspecies, with a large number of differentially expressed genes between the two taxa. In contrast, only ~200 genes were found repeatedly differentially expressed between populations within M. m. musculus that did or did not display assortative mate preferences (close to or more distant from the hybrid zone, respectively), with an overrepresentation of genes belonging to vomeronasal receptor family 2. These receptors are known to play a key role in recognition of chemical cues that handle information about genetic identity. Interestingly, four of five of these differentially expressed receptors belong to the same phylogenetic cluster, suggesting specialization of a group of closely related receptors in the recognition of odorant signals that may allow subspecies recognition and assortative mating.

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e . Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST , PBS, d_xy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.

Transcriptomic differentiation underlying marine-to-freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)

Salinity gradients are critical habitat determinants for freshwater organisms. Silverside fishes in the genus Odontesthes have recently and repeatedly transitioned from marine to freshwater habitats, overcoming a strong ecological barrier. Genomic and transcriptomic changes involved in this kind of transition are only known for a few model species. We present new data and analyses of gene expression and microbiome composition in the gills of two closely related silverside species, marine O. argentinensis and freshwater O. bonariensis and find more than three thousand transcripts differentially expressed, with osmoregulatory/ion transport genes and immune genes showing very different expression patterns across species. Interspecific differences also involve more than one thousand transcripts with nonsynonymous SNPs in the coding sequences, most of which were not differentially expressed. In addition to characterizing gill transcriptomes from wild‐caught marine and freshwater fishes, we test experimentally the response to salinity increases by O. bonariensis collected from freshwater habitats. Patterns of expression in gill transcriptomes of O. bonariensis exposed to high salinity do not resemble O. argentinensis mRNA expression, suggesting lack of plasticity for adaptation to marine conditions in this species. The diversity of functions associated with both the differentially expressed set of transcripts and those with sequence divergence plus marked microbiome differences suggest that multiple abiotic and biotic factors in marine and freshwater habitats are driving transcriptomic differences between these species.

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird species-collared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's ρ = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.

Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L^-1 of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium.

Differential gene expression according to race and host plant in the pea aphid

Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences amongst host races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on numerous plants in the Fabaceae and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host plant, indicating the importance of gene expression in aphid-plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host races may result from genetic drift and reproductive isolation and possibly divergent selection. Expression differences related to plant adaptation include a subset of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies' findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change.

Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae

Hybridization and polyploidization are considered important driving forces that form new epigenetic regulations. To study the changing patterns of expression accompanying hybridization and polyploidization, we used RNA-seq and qRT-PCR to investigate global expression and homoeologue expression in diploid and tetraploid hybrids of Carassius auratus red var. (♀) (R) and Cyprinus carpio (♂) (C). By comparing the relative expression levels between the hybrids and their parents, we defined the expression level dominance (ELD) and homoeologue expression bias (HEB) in liver tissue. The results showed that polyploidization contributed to the conversion of homoeologue ELD. In addition, hybridization had more effect on the change in HEB than polyploidization, while polyploidization had more effect on the change of global gene expression than hybridization. Meanwhile, similar expression patterns were found in growth-related genes. The results suggested that hybridization and polyploidization result in differential degrees of maternal HEB in three tissues (liver, muscle and ovary) tested. The results of this study will increase our understanding of the underlying regulation mechanism of rapid growth in diploid hybrids and allotetraploids. The differential degrees of global expression and homoeologue expression contribute to growth heterosis in newly formed hybrids, ensuring the on-going success of allotetraploid speciation.

Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy

Ecological speciation requires divergent selection, reproductive isolation and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil types and have displaced flowering times, representing an ideal candidate for ecological speciation. We generated large amounts of RNA‐Seq data from multiple individuals and tissue types collected on the island from each of the two species. We found that differentially expressed loci as well as those with divergent coding sequences between Howea species were associated with known ecological and phenotypic differences, including response to salinity, drought, pH and flowering time. From these loci, we identified potential ‘ecological speciation genes’ and further validate their effect on flowering time by knocking out orthologous loci in a model plant species. Finally, we put forward six plausible ecological speciation loci, providing support for the hypothesis that pleiotropy could help to overcome the antagonism between selection and recombination during speciation with gene flow.

Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)

Lectin receptor kinases (LRKs) play a critical role in plants during development and stress conditions, but a comprehensive analysis at genome level is still not carried out in Triticum aestivum. Herein, we performed the genome wide identification, characterization and expression analysis of these genes in T. aestivum (TaLRK). In-total 263 TaLRK genes were identified, which were further classified into three groups based on the nature of lectin domain. We identified, two TaLRKs consisted of calcium-dependent lectin (C-LRK), while 84 legume-lectin (L-LRK) and 177 bulb-lectin (B-LRK) domains. The L-LRK and B-LRK genes were distributed throughout the genome of T. aestivum. Most of the TaLRKs were clustered as homologs, which were distributed either in proximity on same chromosome or on homoeologous chromosomes of A, B and D sub-genomes. A total of 9 and 58 duplication events were also predicted in L-LRK and B-LRK, respectively. Phylogenetic analysis indicated conserved evolutionary relationship of homologous and orthologous genes from multiple plant species. Gene ontology analysis indicated TaLRKs role in binding, signaling and receptor activities. Most of the TaLRKs consisted of a trans-membrane domain and predicted to be localized in the plasma-membrane. A diverse expression pattern of TaLRK genes was found in various developmental stages and stress conditions. Some TaLRKs were found to be highly affected during a particular stress, which indicated a specialized role of each LRK gene in a specific stress condition. These results described various characteristic feature and expression pattern of TaLRK genes, which will pave the way for functional characterization in wheat.

Gene expression in the brain of a migratory songbird during breeding and migration

BACKGROUND

We still have limited knowledge about the underlying genetic mechanisms that enable migrating species of birds to navigate the globe. Here we make an attempt to get insight into the genetic architecture controlling this complex innate behaviour. We contrast the gene expression profiles of two closely related songbird subspecies with divergent migratory phenotypes. In addition to comparing differences in migratory strategy we include a temporal component and contrast patterns between breeding adults and autumn migrating juvenile birds of both subspecies. The two willow warbler subspecies, Phylloscopus trochilus trochilus and P. t. acredula, are remarkably similar both in phenotype and genotype and have a narrow contact zone in central Scandinavia. Here we used a microarray gene chip representing 23,136 expressed sequence tags (ESTs) from the zebra finch Taeniopygia guttata to identify mRNA level differences in willow warbler brain tissue in relation to subspecies and season.

RESULTS

Out of the 22,109 EST probe sets that remained after filtering poorly binding probes, we found 11,898 (51.8 %) probe sets that could be reliably and uniquely matched to a total of 6,758 orthologous zebra finch genes. The two subspecies showed very similar levels of gene expression with less than 0.1 % of the probe sets being significantly differentially expressed. In contrast, 3,045 (13.8 %) probe sets were found to be differently regulated between samples collected from breeding adults and autumn migrating juvenile birds. The genes found to be differentially expressed between seasons appeared to be enriched for functional roles in neuronal firing and neuronal synapse formation.

CONCLUSIONS

Our results show that only few genes are differentially expressed between the subspecies. This suggests that the different migration strategies of the subspecies might be governed by few genes, or that the expression patterns of those genes are time-structured or tissue-specific in ways, which our approach fails to uncover. Our findings will be useful in the planning of new experiments designed to unravel the genes involved in the migratory program of birds.

Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes

Next‐generation sequencing methods, such as RNA‐seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA‐seq annotation methods using reference genomes from related species have yet to be robustly characterized. Here we conduct a comprehensive power analysis employing RNA‐seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcript short reads are aligned directly to the reference genome, significantly outperforms the widely used de novo and guided assembly‐based methods in both the quantity and accuracy of gene detection. Our analysis also reveals that DGM recovers a more representative profile of Gene Ontology functional categories, which are often used to interpret emergent patterns in genomewide expression analyses. Lastly, analysis of available primate RNA‐seq data demonstrates the applicability of our observations across diverse taxa. Our quantification of annotation accuracy and reduced gene detection associated with sequence divergence thus provides empirically derived guidelines for the design of future gene expression studies in species without sequenced genomes.

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species

Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression technology and the paired-end RNA sequencing method, we obtained 21,415 expressed genes across three reproduction-related tissues. Of them, approximately 8% (1,717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1,064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5' flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and provide new insights into the importance of regulatory evolution in ecological speciation in plants.

Unexpected divergence and lack of divergence revealed in continental Asian Cyornis flycatchers (Aves: Muscicapidae)

The flycatcher genus Cyornis (Aves: Muscicapidae) comprises 25 species with Oriental distributions. Their relationships are poorly known. We analyzed the phylogenetic relationships of 70 individuals from 12 species and several subspecies of Cyornis based on three mitochondrial genes and five nuclear introns, with special focus on Chinese and Vietnamese populations of the monotypic C. hainanus and polytypic C. rubeculoides. We found no support for inclusion of C. concretus in Cyornis. Deep divergences were observed among different subspecies of C. banyumas and C. rubeculoides. C. rubeculoides glaucicomans was also shown to have a highly distinctive song, and we propose that it is treated as a distinctive Chinese endemic species, C. glaucicomans. In contrast, the south Vietnamese C. rubeculoides klossi, which has a disjunct distribution from the other subspecies of C. rubeculoides, along with a recently discovered population in Guangdong Province (China) with several plumage features reminiscent of C. r. klossi, were indistinguishable in all loci analyzed from the phenotypically markedly different C. hainanus. More research is needed to elucidate the reasons for this unexpected pattern.

Characterizing a hybrid zone between a cryptic species pair of freshwater snails

Characterizing hybrid zones and their dynamics is a central goal in evolutionary biology, but this is particularly challenging for morphologically cryptic species. The lack of conspicuous divergence between parental types means intermediate hybrid forms often go undetected. We aimed to detect and characterize a suspected hybrid zone between a pair of morphologically cryptic lineages of the freshwater snail, Radix. We sampled Radix from across a contact zone between two mitochondrial lineages (Radix balthica and an undescribed lineage termed 'MOTU3') and detected admixture between two nuclear genotype clusters, which were significantly but not categorically associated with the mitochondrial lineages. Using a model selection approach, we show that the admixture cline is best explained by an interaction between precipitation and temperature gradients over the area, rather than geographic distance. We thus hypothesize that the correlation with climatic gradients suggests environmental selection has played a role in maintaining the hybrid zone. In a 2050 climate change scenario, we furthermore predict an expansion of one of the nuclear clusters and a widening of the hybrid zone as the climate warms and dries.

Comparative expression profiling of three early inflorescence stages of oil palm indicates that vegetative to reproductive phase transition of meristem is regulated by sugar balance

Breeding and seed production activities in oil palm have been hampered because of the inability of the male parent Pisifera to produce male inflorescence as source of pollen under normal conditions. Researchers are using complete defoliation to induce male inflorescences, but the biological and molecular processes responsible for this morphological change are yet to be revealed. To understand the underlying network of genes that initiate and control this phenotypically documented activity, we initiated a study aimed at identifying differentially expressed genes (DEGs) in three stages of an oil palm inflorescence under complete defoliation stress using RNA-seq. Sequencing on an Illumina platform produced 82631476 reads consisting of 8345779076 bases. A total of 60700 genes were obtained after transcript filtering and normalisation and 54% of them were downregulated. Differences in gene expression levels were significant between tissues under stress. The farther the distance between tissues, the more DEGs recorded. Comparison between stage 2 and stage 1 induced 3893 DEGs whereas 10136 DEGs were induced between stage 3 and stage 1. Stress response genes and flower development genes were among the highly expressed genes. This study suggests a link between complete defoliation and meristem differentiation from vegetative to reproductive phase in oil palm.

Whitefly genome expression reveals host-symbiont interaction in amino acid biosynthesis

Background

Whitefly (Bemisia tabaci) complex is a serious insect pest of several crop plants worldwide. It comprises several morphologically indistinguishable species, however very little is known about their genetic divergence and biosynthetic pathways. In the present study, we performed transcriptome sequencing of Asia 1 species of B. tabaci complex and analyzed the interaction of host-symbiont genes in amino acid biosynthetic pathways.

Methodology/Principal Findings

We obtained about 83 million reads using Illumina sequencing that assembled into 72716 unitigs. A total of 21129 unitigs were annotated at stringent parameters. Annotated unitigs were mapped to 52847 gene ontology (GO) terms and 131 Kyoto encyclopedia of genes and genomes (KEGG) pathways. Expression analysis of the genes involved in amino acid biosynthesis pathways revealed the complementation between whitefly and its symbiont partner Candidatus Portiera aleyrodidarum. Most of the non-essential amino acids and intermediates of essential amino acid pathways were supplied by the host insect to its symbiont. The symbiont expressed the pathways for the essential amino acids arginine, threonine and tryptophan and the immediate precursors of valine, leucine, isoleucine and phenyl-alanine. High level expression of the amino acid transporters in the whitefly suggested the molecular mechanisms for the exchange of amino acids between the host and the symbiont.

Conclusions/Significance

Our study provides a comprehensive transcriptome data for Asia 1 species of B. tabaci complex that focusses light on integration of host and symbiont genes in amino acid biosynthesis pathways.

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.

De novo assembly and analysis of crow lungs transcriptome

The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.

Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica

BACKGROUND

The eastern oyster, Crassostrea virginica, is a euryhaline species that can thrive across a wide range of salinities (5-35). As with all estuarine species, individual oysters must be able to regulate their osmotic balance in response to constant temporal variation in salinity. At the population level, recurrent viability selection may be an additional mechanism shaping adaptive osmoregulatory phenotypes at the margins of oyster salinity tolerance. To identify candidate genes for osmoregulation, we sequenced, assembled, and annotated the transcriptome of wild juvenile eastern oysters from 'high' and 'low' salinity regimes. Annotations and candidates were mostly based on the Pacific oyster (Crassostrea gigas) genome sequence so osmoregulatory relevance in C. virginica was explored by testing functional enrichment of genes showing spatially discrete patterns of expression and by quantifying coding sequence divergence.

RESULTS

The assembly of sequence reads and permissive clustering of potentially oversplit alleles resulted in 98,729 reftigs (contigs and singletons). Of these, 50,736 were annotated with 9,307 belonging to a set of candidate osmoregulatory genes identified from the C. gigas genome. A total of 218,777 SNPs (0.0185 SNPs/bp) were identified in annotated reftigs of C. virginica. Amino acid divergence between translations of C. virginica annotated reftigs and C. gigas coding sequence averaged 23.2 % with an average dN/dS ratio of 0.074, suggesting purifying selection on protein sequences. The high and low salinity source oysters each expressed a subset of genes unique to that group, and the functions for these annotated genes were consistent with known molecular mechanisms for osmotic regulation in molluscs.

CONCLUSIONS

Most of the osmoregulatory gene candidates experimentally identified in C. gigas are present in this C. virginica transcriptome. In general these congeners show coding sequence divergence too high to make the C. gigas genome a useful reference for C. virginica bioinformatics. However, strong purifying selection is characteristic of the osmoregulatory candidates so functional annotations are likely to correspond. An initial examination of C. virginica presence/absence expression patterns across the salinity gradient in a single estuary suggests that many of these candidates have expression patterns that co-vary with salinity, consistent with osmoregulatory function in C. virginica.

Reference genes for quantitative gene expression studies in multiple avian species

Quantitative real-time PCR (qPCR) rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM, YWHAZ) on different tissues of the mallard (Anas platyrhynchos), domestic chicken (Gallus gallus domesticus), common crane (Grus grus), white-tailed eagle (Haliaeetus albicilla), domestic turkey (Meleagris gallopavo f. domestica), cockatiel (Nymphicus hollandicus), Humboldt penguin (Sphenicus humboldti), ostrich (Struthio camelus) and zebra finch (Taeniopygia guttata), spanning a broad range of the phylogenetic tree of birds. Primer pairs for six to 11 genes were successfully established for each of the nine species. As a proof of principle, we analyzed expression levels of 10 candidate reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different statistical algorithms, we identified five genes (18S, PGK1, RPS7, TFRC, YWHAZ) that were stably expressed within each group and also between the singing and silent conditions, establishing them as suitable reference genes. In conclusion, the newly developed pan-avian primer set allows accurate normalization and quantification of gene expression levels in multiple avian species.

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution

BACKGROUND

The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. The advent of the next generation sequencing technologies has made it possible to study which genomic regions are evolutionary liable to change and which are static, as well as enabling an increasing number of genome studies of non-model species. However, de novo sequencing of the whole genome of an organism remains non-trivial. In this study, we present the draft genome of the black grouse, which was developed using a reference-guided assembly strategy.

RESULTS

We generated 133 Gbp of sequence data from one black grouse individual by the SOLiD platform and used a combination of de novo assembly and chicken reference genome mapping to assemble the reads into 4572 scaffolds with a total length of 1022 Mb. The draft genome well covers the main chicken chromosomes 1 ~ 28 and Z which have a total length of 1001 Mb. The draft genome is fragmented, but has a good coverage of the homologous chicken genes. Especially, 33.0% of the coding regions of the homologous genes have more than 90% proportion of their sequences covered. In addition, we identified ~1 M SNPs from the genome and identified 106 genomic regions which had a high nucleotide divergence between black grouse and chicken or between black grouse and turkey.

CONCLUSIONS

Our results support the hypothesis that the chromosome X (Z) evolves faster than the autosomes and our data are consistent with the MHC regions being more liable to change than the genome average. Our study demonstrates how a moderate sequencing effort can be combined with existing genome references to generate a draft genome for a non-model species.

Accuracy of allele frequency estimation using pooled RNA-Seq

For nonmodel organisms, genome-wide information that describes functionally relevant variation may be obtained by RNA-Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High-quality genotypes for individual voles, determined for 23,682 SNPs, provided information on 'true' allele frequencies; allele frequencies estimated from the pool were then compared with these values. 'True' frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in gene expression and allele-specific gene expression influencing allele frequency estimation accuracy. Moreover, we observed strong negative relationship between minor allele frequency and relative estimation error. Our results indicate that pooled RNA-Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. This should help in taking account the difference in accuracy between conservatively expressed transcripts and these which are variable in expression level.

An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone

Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (∼3 loci per gene, totalling 60 kb) in population samples of crows (n=23 for each taxon). Tajima's D, Fu's FS, DHEW and HKA (Hudson-Kreitman-Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4Ner∼0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.

Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa

Understanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphratica, which diverged in the recent past. Following an approach taken previously with P. euphratica, we conducted a deep transcriptomic analysis of P. pruinosa. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of two types of callus and desert-grown trees. De novo assembly generated 114,866 high-quality unique sequences using Solexa sequence data. Following assembly we were able to identify, with high confidence, 2859 orthologous sequence pairs between the two species. Based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, we identified a total of 84 (2.9%) ortholog pairs exhibiting rapid evolution with signs of strong selection (Ka/Ks>1). Genes homologous to these ortholog pairs in model species are mainly involved in ‘responses to stress’, ‘ubiquitin-dependent protein catabolic processes’, and ‘biological regulation’. Finally, we examined the expression patterns of candidate genes with rapid evolution in response to salt stress. Only one pair of orthologs up-regulated their expression in both species while three and four genes were found to up-regulated in P. pruinosa and in P. euphratica respectively. Our findings together suggest that the genes at the same category or network but with differentiated expressions or functions may have evolved rapidly during adaptive divergence of the two species to differentiated salty desert habitats.