Temporal transcriptional variation is a major contributor to functional evolution and the developmental process. Parthenogenetic water fleas of the genus Daphnia (Cladocera) provide an ideal model to ...characterize gene expression patterns across distinct developmental stages. Herein, we report RNA-seq data for female Daphnia mitsukuri at three developmental stages: the embryo, juvenile (three timepoints) and adult. Comparisons of gene expression patterns among these three developmental stages and weighted gene co-expression network analysis based on expression data across developmental stages identified sets of genes underpinning each of the developmental stages of D. mitsukuri. Specifically, highly expressed genes (HEGs) at the embryonic developmental stage were associated with cell proliferation, ensuring the necessary foundation for subsequent development; HEGs at the juvenile stages were associated with chemosensory perception, visual perception and neurotransmission, allowing individuals to enhance detection of potential environmental risks; HEGs at the adult stage were associated with antioxidative defensive systems, enabling adults to mount an efficient response to perceived environmental risks. Additionally, we found a significant overlap between expanded gene families of Daphnia species and HEGs at the juvenile stages, and these genes were associated with visual perception and neurotransmission. Our work provides a resource of developmental transcriptomes, and comparative analyses that characterize gene expression dynamics throughout development of Daphnia.
Display omitted
•Two distinct species complexes (D. pulex and D. mitsukuri) were documented.•Strikingly different patterns of clonal diversity were observed among populations.•Obligate ...parthenogenesis was confirmed by genotyping dormant ephippial eggs.•Obligate parthenogens probably originated through interspecific hybridization.
Recent studies of the distribution and diversity of freshwater zooplankton have indicated that the previously understudied Eastern Palearctic region is an important biogeographic hotspot. Here, we explored the lineage diversity and reproductive modes of the Daphnia pulex species group across China. Members of this group are often keystone species of standing water bodies and are frequently used as a model system for ecological, evolutionary and, more recently, genomic studies. We found members of the D. pulex group in seven of seventy-six Chinese water bodies examined. We analyzed their phylogenetic position using mitochondrial markers, and explored the genetic structure of six populations using microsatellite markers. Mitochondrial DNA analysis suggested the presence of two distinct species complexes in China: the D. pulex complex that has a global distribution, and an apparently endemic Eastern Palearctic D. mitsukuri complex. Microsatellite analyses of six populations suggested that three of these reproduced by cyclical parthenogenesis, as evidenced by high clonal diversity and the absence of deviations from the Hardy-Weinberg equilibrium. In contrast, three other populations showed remarkably low diversity of multilocus genotypes. This suggests an obligate parthenogenetic reproductive mode, which was confirmed in one of the populations by comparison of genotypes of Daphnia adults and dormant embryos. All presumably obligate parthenogenetic clones were heterozygous at the majority of microsatellite loci, suggesting their hybrid origin. This was further supported by analyses of a small GTPase nuclear gene (rab4), as two alleles within single individuals belonged to different clades. Interestingly, one putatively obligate parthenogenetic clone carried three distinct alleles suggesting higher ploidy and potential gene flow between the D. pulicaria and D. mitsukuri complexes. Our data show that the expansion of the D. pulex complex in the Eastern Palearctic was associated with widespread hybridization.
Display omitted
•We explored lineage diversity and regional distribution of Moina in China.•Four Moina species complexes with eleven mtDNA lineages occurred across China.•Discordance between mtDNA ...and nuclear ITS-1 phylogenies of Moina was detected.•An mtDNA phylogeny showed apparent paraphyly in two Moina taxa.
The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1). Both molecular markers identified four clades corresponding broadly to the morphological species. Mitochondrial DNA analysis showed the presence of four species complexes with eleven lineages across China, five of which were new. However, some lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. In contrast, a few lineages exhibited restricted distributions. The nuclear phylogeny also recognized four species of Moina within China and seven very distinct clades. Interestingly, one specimen possessing Moina cf. micrura mtDNA had ITS-1 alleles of the M. cf. brachiata clade. This discordance between mtDNA and nuclear ITS-1 phylogenies is indicative of interspecific introgression and hybridization. Additionally, our COI phylogeny showed apparent paraphyly in two Moina species groups, suggesting introgression of their mitochondrial genomes. Our data shows the regional distribution/diversity of the Moina species complex in a Eurasian context.
Fairy shrimp are the most divergent taxon of large branchiopod crustaceans and have a worldwide distribution. Yet the diversity and distribution of fairy shrimps in the “Roof of the World” remain ...poorly known. Here, based on morphology, we identified three species of fairy shrimp (
Branchinecta orientalis
,
Chirocephalus graziellae
and
Branchipodopsis affinis
), among 14 fairy-shrimp populations from the Tibetan Plateau, China. Their phylogenetic relationships were verified based on mitochondrial DNA sequences (cytochrome
c
oxidase subunit I gene) and two nuclear markers (18S ribosomal RNA gene and internal transcribed spacer 2). Syntopy of different species of fairy shrimp was observed. Some haplotypes were shared among populations, and sequences from
B. affinis
exhibited a star-like pattern in haplotype networks, suggesting a recent rapid expansion. Finally, a high genetic diversity of fairy shrimp was detected on the Tibetan Plateau. Obtained results contribute to a better knowledge of the diversity of high-altitude fairy shrimps.
Electroencephalography (EEG) based emotion recognition enables machines to perceive users' affective states, which has attracted increasing attention. However, most of the current emotion recognition ...methods neglect the structural information among different brain regions, which can lead to the incorrect learning of high-level EEG feature representation. To mitigate possible performance degradation, we propose a novel nuclear norm regularized deep neural network framework (NRDNN) that can capture the structural information among different brain regions in EEG decoding. The proposed NRDNN first utilizes deep neural networks to learn high-level feature representations of multiple brain regions, respectively. Then, a set of weights indicating the contributions of each brain region can be automatically learned using a region-attention layer. Subsequently, the weighted feature representations of multiple brain regions are stacked into a feature matrix, and the nuclear norm regularization is adopted to learn the structural information within the feature matrix. The proposed NRDNN method can learn the high-level representations of EEG signals within multiple brain regions, and the contributions of them can be automatically adjusted by assigning a set of weights. Besides, the structural information among multiple brain regions can be captured in the learning procedure. Finally, the proposed NRDNN can perform in an efficient end-to-end manner. We conducted extensive experiments on publicly available emotion EEG dataset to evaluate the effectiveness of the proposed NRDNN. Experimental results demonstrated that the proposed NRDNN can achieve state-of-the-art performance by leveraging the structural information.
Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. ...japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.
In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.
Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.
The evolution and adaptation of S. japonicum, a zoonotic parasite that causes human schistosomiasis, remain unclear because of the lack of whole-genome data. We construct a chromosome-level ...S. japonicum genome and analyze it together with 72 samples representing six populations of the entire endemic region. We observe a Taiwan zoophilic lineage splitting from zoonotic populations ∼45,000 years ago, consistent with the divergent history of their intermediate hosts. Interestingly, we detect a severe population bottleneck in S. japonicum, largely coinciding with human history in Asia during the last glacial maximum. We identify several genomic regions underlying natural selection, including GATAD2A and Lmln, both showing remarkable differentiation among different areas. RNAi knockdown suggests association of GATAD2A with parasite development and infection in definitive hosts, while Lmln relates to the specificity of the intermediate hosts. Our study provides insights into the evolution of S. japonicum and serves as a resource for further studies.
Display omitted
•De novo assembly of a Schistosoma japonicum genome as well as 72 re-sequenced genomes•Analysis of genetic structure and adaptive evolution of six S. japonicum populations•Dissection of the genetic basis of host switching•A genomic resource for further studies of S. japonicum
Luo et al. assemble a high-quality reference genome of S. japonicum and re-sequence 72 genomes covering the entire endemic regions. This study presents the genetic diversity and evolutionary history of six S. japonicum populations, as well as the genetic basis of host switching, with implications for schistosomiasis control.
Display omitted
► Genetic structures of two
Daphnia communities infected by microparasites were surveyed. ► Clonal composition significantly differed between random (infected and uninfected) and ...infected sub-samples. ► In a multi-taxon community, one of the host species was consistently under-infected. ► Parasite-driven selection is a strong factor affecting natural
Daphnia populations.
Numerous theoretical studies suggest that parasites impose a strong selection pressure on their host, driving genetic changes within host populations. Yet evidence of this process in the wild is scarce. In the present study we surveyed, using high resolution microsatellite markers, the genetic structure of cyclically parthenogenetic
Daphnia hosts within two different
Daphnia communities belonging to the
Daphnia longispina hybrid complex. One community, consisting of a single host species, was infected with the protozoan parasite
Caullerya mesnili. The second community consisted of two parental
Daphnia spp. and their hybrids, and was infected with the yeast parasite
Metschnikowia. Significant differences in the clonal composition between random and infected sub-samples of
Daphnia were detected on several occasions within both communities, indicating that host genotypes differ in resistance to both parasites. In addition, one parental species in the multi-taxon community was consistently under-infected, compared with the other taxa. Overall, our field data confirm that infection patterns are strongly affected by host genetic composition in various
Daphnia–microparasite systems. Thus, parasite-driven selection operates in natural
Daphnia populations and microparasites influence the clonal structure of host populations.
The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing ...eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci.
Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe.
Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.
Copepods are key components of aquatic ecosystems and can help regulate the global carbon cycle. Much attention has been paid to the species diversity of copepods worldwide, but the phylogeography ...and genetic diversity of copepods in Nigeria is unexplored.
Using a mitochondrial cytochrome c oxidase subunit I marker, we preformed phylogenetic and phylogeographic analyses for Cyclopidae copepods in Southeast Nigeria. A high species diversity of Cyclopidae in Nigeria: 5 species of Tropocyclops, 5 species of Mesocyclops and 2 species of Thermocyclops from Cyclopidae were identified in 15 populations. Moreover, we detected 18 unique haplotypes, which fell into two distinct clades. Pairwise genetic distances (uncorrected p-distances) among the species of Cyclopidae ranged from 0.05 to 0.257. Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. Finally, we found that the population genetic diversity for each species of Cyclopidae was low in Nigeria.
Our findings explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems: a high species diversity of Cyclopidae copepods was detected over a small geographic sampling range. Results from this study contribute to a better understanding of copepod diversity of Nigerian freshwater ecosystems.
PDF
