Positively Selected Genes Research Articles

Comparative Analyses Reveal the Genetic Mechanism of Ambergris Production in the Sperm Whale Based on the Chromosome-Level Genome.

Sperm whales are a marine mammal famous for the aromatic substance, the ambergris, produced from its colon. Little is known about the biological processes of ambergris production, and this study aims to investigate the genetic mechanism of ambergris production in the sperm whale based on its chromosome-level genome. Comparative genomics analyses found 1207 expanded gene families and 321 positive selected genes (PSGs) in the sperm whale, and functional enrichment analyses suggested revelatory pathways and terms related to the metabolism of steroids, terpenoids, and aldosterone, as well as microbiota interaction and immune network in the intestine. Furthermore, two sperm-whale-specific missense mutations (Tyr393His and Leu567Val) were detected in the PSG LIPE, which has been reported to play vital roles in lipid and cholesterol metabolism. In total, 46 CYP genes and 22 HSD genes were annotated, and then mapped to sperm whale chromosomes. Furthermore, phylogenetic analysis of CYP genes in six mammals found that CYP2E1, CYP51A and CYP8 subfamilies exhibited relative expansion in the sperm whale. Our results could help understand the genetic mechanism of ambergris production, and further reveal the convergent evolution pattern among animals that produce similar odorants.

A chromosome-level genome assembly of theHenosepilachna vigintioctomaculataprovides insights into the evolution of ladybird beetles

The ladybird beetle Henosepilachna vigintioctomaculata is an economically significant oligophagous pest that induces damage to many Solanaceae crops. An increasing number of studies have examined the population and phenotype diversity of ladybird beetles. However, few comparative genome analyses of ladybird beetle species have been conducted. Here, we obtained a high-quality chromosome-level genome assembly of H. vigintioctomaculata using various sequencing technologies, and the chromosome-level genome assembly was ~581.63 Mb, with 11 chromosomes successfully assembled. The phylogenetic analysis showed that H. vigintioctomaculata is a more ancient lineage than the other three sequenced ladybird beetles, Harmonia axyridis, Propylea japonica, and Coccinella septempunctata. We also compared positively selected genes (PSGs), transposable elements (TEs) ratios and insertion times, and key gene families associated with environmental adaptation among these ladybird beetles. The pattern of TEs evolution of H. vigintioctomaculata differs from the other three ladybird beetles. The PSGs were associated with ladybird beetles development. However, the key gene families associated with environmental adaptation in ladybird beetles varied. Overall, the high-quality draft genome sequence of H. vigintioctomaculata provides a useful resource for studies of beetle biology, especially for the invasive biology of ladybird beetles.

Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species.

Due to the difficulty in accurately identifying structural variants (SVs) across genomes, their impact on cis-regulatory divergence of closely related species, especially fish, remains to be explored. Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes. However, the role of broad H3K4me3 domains in phenotypic divergence remains poorly understood. Siniperca chuatsi and S. scherzeri are closely related but divergent in several phenotypic traits, making them an ideal model to study cis-regulatory evolution in sister species. Here, we generated chromosome-level genomes of S. chuatsi and S. scherzeri, with assembled genome sizes of 716.35 and 740.54 Mb, respectively. The evolutionary histories of S. chuatsi and S. scherzeri were studied by inferring dynamic changes in ancestral population sizes. To explore the genetic basis of adaptation in S. chuatsi and S. scherzeri, we performed gene family expansion and contraction analysis and identified positively selected genes (PSGs). To investigate the role of SVs in cis-regulatory divergence of closely related fish species, we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of S. chuatsi and S. scherzeri. Integrated analysis revealed that cis-regulatory divergence caused by SVs played an essential role in phenotypic divergence between S. chuatsi and S. scherzeri. Additionally, divergent broad H3K4me3 domains were mostly associated with cancer-related genes in S. chuatsi and S. scherzeri and contributed to their phenotypic divergence.

Comparative analysis of mitochondrial genomes reveals marine adaptation in seagrasses

BackgroundSeagrasses are higher marine flowering plants that evolved from terrestrial plants, but returned to the sea during the early evolution of monocotyledons through several separate lineages. Thus, they become a good model for studying the adaptation of plants to the marine environment. Sequencing of the mitochondrial (mt) genome of seagrasses is essential for understanding their evolutionary characteristics.ResultsIn this study, we sequenced the mt genome of two endangered seagrasses (Zostera japonica and Phyllospadix iwatensis). These data and data on previously sequenced mt genomes from monocotyledons provide new evolutionary evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. The mt genomes of Z. japonica and P. iwatensis are circular. The sizes of the three seagrasses (including Zostera marine) that have been sequenced to date are smaller than that of other monocotyledons. Additionally, we found a large number of repeat sequences in seagrasses. The most abundant long repeat sequences were 31–40 bp repeats. Our study also found that seagrass species lost extensive ribosomal protein genes during evolution. The rps7 gene and the rpl16 gene of P. iwatensis are exceptions to this trend. The phylogenetic analysis based on the mt genome strongly supports the previous results. Furthermore, we identified five positive selection genes (atp8, nad3, nad6, ccmFn, and matR) in seagrasses that may be associated with their adaptation to the marine environment.ConclusionsIn this study, we sequenced and annotated the mt genomes of Z. japonica and P. iwatensis and compared them with the genome of other monocotyledons. The results of this study will enhance our understanding of seagrass adaptation to the marine environment and can inform further investigations of the seagrass mt genome.

Genomic divergence between two sister Ostrya species through linked selection and recombination.

Studying the evolution of genomic divergence between lineages is a topical issue in evolutionary biology. However, the evolutionary forces that shape the heterogeneous divergence of the genomic landscape are still poorly understood. Here, two wind-pollinated sister-species (Ostrya japonica and O. chinensis) are used to explore what these potential forces might be. A total of 40 individuals from 16 populations across their main distribution areas in China were sampled for genome-wide resequencing. Population demography analyses revealed that these two sister-species diverged at 3.06-4.43 Mya. Both population contraction and increased gene flow were detected during glacial periods, suggesting secondary contact at those times. All three parameters (D XY, π, and ρ) decreased in those regions showing high levels of differentiation (F ST). These findings indicate that linked selection and recombination played a key role in the genomic heterogeneous differentiation between the two Ostrya species. Genotype-environment association analyses showed that precipitation was the most important ecological factor for speciation. Such environmentally related genes and positive selection genes may have contributed to local adaptation and the maintenance of species boundaries.

Identification of Key Genes and Pathways Associated with Preeclampsia by a WGCNA and an Evolutionary Approach.

Preeclampsia (PE) is the serious obstetric-related disease characterized by newly onset hypertension and causes damage to the kidneys, brain, liver, and more. To investigate genes with key roles in PE's pathogenesis and their contributions, we used a microarray dataset of normotensive and PE patients and conducted a weighted gene co-expression network analysis (WGCNA). Cyan and magenta modules that are highly enriched with differentially expressed genes (DEGs) were revealed. By using the molecular complex detection (MCODE) algorithm, we identified five significant clusters in the cyan module protein-protein interaction (PPI) network and nine significant clusters in the magenta module PPI network. Our analyses indicated that (i) human accelerated region (HAR) genes are enriched in the magenta-associated C6 cluster, and (ii) positive selection (PS) genes are enriched in the cyan-associated C3 and C5 clusters. We propose these enriched HAR and PS genes, i.e., EIF4E, EIF5, EIF3M, DDX17, SRSF11, PSPC1, SUMO1, CAPZA1, PSMD14, and MNAT1, including highly connected hub genes, HNRNPA1, RBMX, PRKDC, and RANBP2, as candidate key genes for PE's pathogenesis. A further clarification of the functions of these PPI clusters and key enriched genes will contribute to the discovery of diagnostic biomarkers for PE and therapeutic intervention targets.

Characterization of the Chloroplast Genome Structure of Gueldenstaedtia verna (Papilionoideae) and Comparative Analyses among IRLC Species

The genus Gueldenstaedtia belongs to Papilionaceae’s inverted repeat-lacking clade (IRLC) and includes four species distributed throughout Asia. We sequenced the chloroplast genome of G. verna and compared it with those of the IRLC clade. The genome was 122,569 bp long, containing 77 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analyses showed that G. verna lost one inverted repeat region, the rps16 gene, an intron of rpoC1, and two introns of clpP. Additionally, G. verna had four inversions (~50 kb inversion, trnK–psbK; ~28 kb inversion, accD–rpl23; ~10 kb inversion, rps15–trnL; ~6 kb inversion, trnL–trnI) and one reposition (ycf1). Its G + C content was higher than that of other IRLC species. The total length and number of repeats of G. verna were not significantly different from those of the other IRLC species. Phylogenetic analyses showed that G. verna was closely related to Tibetia. A comparison of substitution rates showed that ycf2 and rps7 were higher than one, suggesting that these were positive selection genes, while others were related to purified selection. This study reports the structure of the chloroplast genome of a different type, i.e., with four inversions and one reposition, and would be helpful for future research on the evolution of the genome structure of the IRLC.

Chromosome-level genome assembly of the bar-headed goose (Anser indicus)

Bar-headed geese (Anser indicus) are adaptable to plateau environments. In this study, we sequenced and assembled a high-quality chromosome-level genome of the bar-headed goose using PacBio long reads and Hi-C technique, and generated 115.73 Gb of Illumina short-reads and 95.89 Gb of PacBio long-reads. The assembled bar-headed goose genome, with a contig N50 of 5.734 Mb and a scaffold N50 of 65.77 Mb, is 1.129 Gb in length and includes 33 chromosomes and 451 fragments. BUSCO assessment yielded a completeness score of 94.4%. In total, 15,376 protein-coding genes were predicted, of which 94.95% had homologs in protein databases. We identified 78 positively selected genes (PSGs) in the bar-headed goose genome, which were mainly enriched in calcium ion and ATP-binding. This bar-headed goose genome will be an important resource for increasing our understanding regarding the genetic basis of adaptation to life at a high altitude.

Discovery of exercise-related genes and pathway analysis based on comparative genomes of Mongolian originated Abaga and Wushen horse.

The Mongolian horses have excellent endurance and stress resistance to adapt to the cold and harsh plateau conditions. Intraspecific genetic diversity is mainly embodied in various genetic advantages of different branches of the Mongolian horse. Since people pay progressive attention to the athletic performance of horse, we expect to guide the exercise-oriented breeding of horses through genomics research. We obtained the clean data of 630,535,376,400 bp through the entire genome second-generation sequencing for the whole blood of four Abaga horses and ten Wushen horses. Based on the data analysis of single nucleotide polymorphism, we severally detected that 479 and 943 positively selected genes, particularly exercise related, were mainly enriched on equine chromosome 4 in Abaga horses and Wushen horses, which implied that chromosome 4 may be associated with the evolution of the Mongolian horse and athletic performance. Four hundred and forty genes of positive selection were enriched in 12 exercise-related pathways and narrowed in 21 exercise-related genes in Abaga horse, which were distinguished from Wushen horse. So, we speculated that the Abaga horse may have oriented genes for the motorial mechanism and 21 exercise-related genes also provided a molecular genetic basis for exercise-directed breeding of the Mongolian horse.

Cold Resistance of Euonymus japonicus Beihaidao Leaves and Its Chloroplast Genome Structure and Comparison with Celastraceae Species.

Euonymus japonicus Beihaidao is one of the most economically important ornamental species of the Euonymus genus. There are approximately 97 genera and 1194 species of plants worldwide in this family (Celastraceae). Using E. japonicus Beihaidao, we conducted a preliminary study of the cold resistance of this species, evaluated its performance during winter, assembled and annotated its chloroplast genome, and performed a series of analyses to investigate its gene structure GC content, sequence alignment, and nucleic acid diversity. Our objectives were to understand the evolutionary relationships of the genus and to identify positive selection genes that may be related to adaptations to environmental change. The results indicated that E. japonicus Beihaidao leaves have certain cold resistance and can maintain their viability during wintering. Moreover, the chloroplast genome of E. japonicus Beihaidao is a typical double-linked ring tetrad structure, which is similar to that of the other four Euonymus species, E. hamiltonianus, E. phellomanus, E. schensianus, and E. szechuanensis, in terms of gene structure, gene species, gene number, and GC content. Compared to other Celastraceae species, the variation in the chloroplast genome sequence was lower, and the gene structure was more stable. The phylogenetic relationships of 37 species inferred that members of the Euonymus genus do not form a clade and that E. japonicus Beihaidao is closely related to E. japonicus and E. fortunei. A total of 11 functional positive selected genes were identified, which may have played an important role in the process of Celastraceae species adapting to environmental changes. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Celastraceae species.

Comparative Genome Analysis Reveals the Genomic Basis of Semi-Aquatic Adaptation in American Mink (Neovison vison).

Simple SummaryIn nature, every animal lives in its suitable environment to support life and reproduction. Due to survival pressure, the ancient ancestors of land animals changed from living in water to living on land through a long time of evolution. But as more and more animals live on land, the pressure to survive increases, and some animals continue to evolve and re-enter the water. Species evolved from water to land, fins became limbs, and re-entering organisms evolved webbing, all in an effort to better adapt to their environment. The American mink’s life is extremely dependent on the water environment, but its external changes are less pronounced than those of other water-dependent animals. Since the limited external changes are not sufficient to indicate that the American mink is a semi-aquatic mammal, we can explore the evidence of aquatic adaptation at the molecular level. Through comparative genomic analysis, we obtained that American mink has certain adaptive evolution to aquatic environment in olfactory, coagulation, immunity and other aspects. The results of this study have important reference significance for exploring biological evolution and species conservation.Although the American mink is extremely dependent on water and has evolved a range of aquatic characteristics, its structural adaptation to water is still less obvious than that of other typical semi-aquatic mammals, such as otters. Therefore, many scholars consider it not to be a semi-aquatic mammal. In order to make the point that minks are semi-aquatic mammals more convincing, we provide evidence at the micro (genome)-level. In particular, we used the genomes of the American mink and 13 mammalian species to reconstruct their evolutionary history, identified genes that affect aquatic adaptation, and examined the evolution of aquatic adaptation. By analyzing unique gene families, the expansion and contraction of gene families, and positive selection genes, we found that the American mink genome has evolved specifically for aquatic adaptation. In particular, we found that the main adaptive characteristics of the American mink include the external structural characteristics of bone and hair development, as well as the internal physiological characteristics of immunity, olfaction, coagulation, lipid metabolism, energy metabolism, and nitrogen metabolism. We also observed that the genomic characteristics of the American mink are similar to those of other aquatic and semi-aquatic mammals. This not only provides solid genomic evidence for the idea that minks are semi-aquatic mammals, but also leads to a clearer understanding of semi-aquatic species. At the same time, this study also provides a reference for the protection and utilization of the American mink.

Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing.

Simple SummaryThe size of antlers varies among species; antlers of the wapiti (Cervus canadensis xanthopygus) grow much faster than those of its close relative the sika deer (Cervus nippon hortulorum) in the same growing period. This contrast provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, the reference transcriptomes of the antler reserve mesenchyme (RM) tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared, and interactive relationships and expression patterns of hub genes were identified and analysed. We identified that RNA Binding Motif Protein X-Linked (RBMX) gene was under strongly positive selection. One gene found to interact with RBMX was methyltransferase-like 3 (METTL3), an oncogene that could promote translation of cancer cell proteins. There was a contrasting relationship in expression level between RBMX and METTL3 genes in the RM tissue. We believe our study can provide a better understanding of rapid antler growth at the molecular level in particular and endochondral ossification in general.The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcriptomes of antler RM tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared. The results showed that: a total of 44,485 reference full-length transcripts of antlers were obtained; 254 highly expressed transcripts (HETs) and 1936 differentially expressed genes (DEGs) were enriched and correlated principally with translation, endochondral ossification and ribosome; 228 genes were found to be under strong positive selection and would thus be important for the evolution of wapiti and sika deer; among the alternative splicing variants, 381 genes were annotated; and 4 genes with node degree values greater than 50 were identified through interaction network analysis. We identified a negative and a positive regulator for rapid antler growth, namely RNA Binding Motif Protein X-Linked (RBMX) and methyltransferase-like 3 (METTL3), respectively. Overall, we took advantage of this significant difference in growth rate and performed the comparative analyses of the antlers to identify key specific factors that might be candidates for the positive or negative regulation of phenomenal antler growth rate.

Insights into adaptive divergence of Japanese mantis shrimp Oratosquilla oratoria inferred from comparative analysis of full-length transcriptomes

The heterogeneous seascapes in the northwestern Pacific (NWP) can be important selective forces driving adaptive divergence of marine coastal species distributed along the gradients. Here, we tested this hypothesis in Japanese mantis shrimp (Oratosquilla oratoria) with a wide distribution in the NWP and a significant north-south population structure. To this end, the full-length (FL) transcriptomes of northern and southern O. oratoria were firstly sequenced using PacBio single molecule real-time sequencing technology. Based on the FL transcriptome data, we captured large-scale FL transcripts of O. oratoria and predicted the FL transcriptome structure, including coding region, transcription factor and long noncoding RNA. To reveal the divergence between northern and southern O. oratoria, we identified 2,182 pairs of orthologous genes and inferred their sequence divergences. The average differences in coding, 5’ untranslated and 3’ untranslated region were 1.44%, 2.79% and 1.46%, respectively, providing additional support to previous proposition that northern and southern O. oratoria are two species. We provided further evolutionary context to our analysis by identifying positive selected genes (PSGs) between northern and southern O. oratoria. In total, 98 orthologs were found evolving under positive selection and involved several environmentally responsive genes associated with stress response, immunity and cytoskeletal organization, etc. Furthermore, we found PSGs also diverged in gene expression response of northern and southern O. oratoria to heat stress. These findings not only highlight the importance of genetic variation in these genes in adapting to environmental changes in O. oratoria, but also suggest that natural selection may act on the plasticity of gene expression to facilitate O. oratoria adaptation to environmental gradients. Overall, our work contributes to understanding how marine coastal species has evolved to adapt to heterogeneous seascapes in the NWP.

Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions.

Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.

Patterns and impacting factors of gene evolutionary rate between wild and cultivated emmer wheat (Triticum turgidum)

AbstractTetraploid emmer wheat (Triticum turgidum L., BBAA) is the founder progenitor of bread wheat, providing the valuable genetic resource and gene pool for wheat improvement. However, the evolutionary trajectory of tetraploid wheat, especially the evolutionary fate of different types of genes has not been well studied. In this study, the rate of non‐synonymous substitution (dN) and synonymous substitution (dS) was calculated by comparing the orthologs between the wild emmer and cultivated durum wheat at the whole genome and subgenome levels to obtain the positively selected genes (PSGs) and negatively selected genes (NSGs). Then, mutation rate, gene length, exon number, GC content, codon bias, and expression level were comprehensively investigated and compared between the PSGs and NSGs. Within both wild emmer and cultivated durum wheat, PSGs between A and B subgenome displayed shorter gene and exon lengths as well as fewer exon numbers compared with NSGs, whereas from wild emmer to cultivated durum wheat, PSGs showed longer gene length and more exon numbers. Furthermore, PSGs displayed much higher expression levels and stronger codon usage bias, but lower genetic diversity compared with NSGs. Finally, two PSGs TdER1‐6B, and TdLC7‐2A, were found to play the crucial roles in regulating grain width and plant height of tetraploid wheat, respectively. This study systematically investigated the evolutionary, structural, and functional difference between PSGs and NSGs in tetraploid wheat, which will contribute to a better understanding of the selective mode and evolutionary trajectory during wheat domestication and evolution.

Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains

Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.

Genomic insights into positive selection during barley domestication

BackgroundCultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process.ResultsThe rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs. landrace and landrace vs. improved cultivar). The rates of evolution, properties, expression patterns, and diversity of positively selected genes (PSGs) and negatively selected genes (NSGs) were compared. PSGs evolved more rapidly, possessed fewer exons, and had lower GC content than NSGs; they were also shorter and had shorter intron, exon, and first exon lengths. Expression levels were lower, the tissue specificity of expression was higher, and codon usage bias was weaker for PSGs than for NSGs. Nucleotide diversity analysis revealed that PSGs have undergone a more severe genetic bottleneck than NSGs. Several candidate PSGs were involved in plant growth and development, which might make them as excellent targets for the molecular breeding of barley.ConclusionsOur comprehensive analysis of the evolutionary, structural, and functional divergence between PSGs and NSGs in barley provides new insight into the evolutionary trajectory of barley during domestication. Our findings also aid future functional studies of PSGs in barley.

Chromosome-Level Genome Assembly of Acanthogobius ommaturus Provides Insights Into Evolution and Lipid Metabolism

Acanthogobius ommaturus is a large, fast-growing annual fish widely distributed in coastal and estuarine areas. The adults will die after breeding, and its life cycle is only 1 year. The first chromosome-level genome assembly of A. ommaturus was obtained by PacBio and Hi-C sequencing in this study. The final genome assembly after Hi-C correction was 921.49 Mb, with contig N50 and scaffold N50 values of 15.70 Mb and 40.99 Mb, respectively. The assembled sequences were anchored to 22 chromosomes by using Hi-C data. A total of 18,752 protein-coding genes were predicted, 97.90% of which were successfully annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results for genome and gene annotations were 93.6% and 84.6%, respectively. A. ommaturus is phylogenetically closely related to Periophthalmodon magnuspinnatus and Boleophthalmus pectinirostris, diverging approximately 31.9 MYA with the two goby species. The A. ommaturus genome displayed 597 expanded and 3,094 contracted gene families compared with the common ancestor. A total of 1,155 positive selected genes (PSGs) (p < 0.05) were identified. Based on comparative genomic analyses, we obtained several expanded genes such as acsbg2, lrp1, lrp6, and znf638 involved in lipid metabolism. A total of twenty candidate genes were identified under positive selection, which associated with lifespan including ercc6, igf1, polg, and tert. Interspecific collinearity analysis showed a high genomic synteny between A. ommaturus and P. magnuspinnatus. The effective population size of A. ommaturus decreased drastically during 200–100 Ka because of Guxiang ice age and then increased gradually following warm periods. This study provides pivotal genetic resources for in-depth biological and evolutionary studies, and underlies the molecular basis for lipid metabolism.

Full-Length Transcriptome Comparison Provides Novel Insights into the Molecular Basis of Adaptation to Different Ecological Niches of the Deep-Sea Hydrothermal Vent in Alvinocaridid Shrimps

The deep-sea hydrothermal vent ecosystem is one of the extreme chemoautotrophic environments. Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, and Alvinocaris longirostris Kikuchi and Ohta, 1995, are typically co-distributed and closely related alvinocaridid shrimps in hydrothermal vent areas with different ecological niches, providing an excellent model for studying the adaptive evolution mechanism of animals in the extreme deep-sea hydrothermal vent environment. The shrimp S. leurokolos lives in close proximity to the chimney vent discharging high-temperature fluid, while A. longirostris inhabits the peripheral areas of hydrothermal vents. In this study, full-length transcriptomes of S. leurokolos and A. longirostris were generated using a combination of single-molecule real-time (SMRT) and Illumina RNA-seq technology. Expression analyses of the transcriptomes showed that among the top 30% of highly expressed genes of each species, more genes related to sulfide and heavy metal metabolism (sulfide: quinone oxidoreductase, SQR; persulfide dioxygenase, ETHE1; thiosulfate sulfurtransferase, TST, and ferritin, FRI) were specifically highly expressed in S. leurokolos, while genes involved in maintaining epibiotic bacteria or pathogen resistance (beta-1,3-glucan-binding protein, BGBP; endochitinase, CHIT; acidic mammalian chitinase, CHIA, and anti-lipopolysaccharide factors, ALPS) were highly expressed in A. longirostris. Gene family expansion analysis revealed that genes related to anti-oxidant metabolism (cytosolic manganese superoxide dismutase, SODM; glutathione S-transferase, GST, and glutathione peroxidase, GPX) and heat stress (heat shock cognate 70 kDa protein, HSP70 and heat shock 70 kDa protein cognate 4, HSP7D) underwent significant expansion in S. leurokolos, while CHIA and CHIT involved in pathogen resistance significantly expanded in A. longirostris. Finally, 66 positively selected genes (PSGs) were identified in the vent shrimp S. leurokolos. Most of the PSGs were involved in DNA repair, antioxidation, immune defense, and heat stress response, suggesting their function in the adaptive evolution of species inhabiting the extreme vent microhabitat. This study provides abundant genetic resources for deep-sea invertebrates, and is expected to lay the foundation for deep decipherment of the adaptive evolution mechanism of shrimps in a deep-sea chemosynthetic ecosystem based on further whole-genome comparison.

Transcriptome analysis provides new insights into cold adaptation of corsac fox (Vulpes Corsac).

Vulpesare widely distributed throughout the world and have undergone drastic physiological and phenotypic changes in response to their environment. However, little is known about the underlying genetic causes of these traits, especially Vulpes corsac. In this study, RNA‐Seq was used to obtain a comprehensive dataset for multiple pooled tissues of corsac fox, and selection analysis of orthologous genes was performed to identify the genes that may be influenced by the low‐temperature environment. More than 6.32 Gb clean reads were obtained and assembled into a total of 173,353 unigenes with an average length of 557 bp for corsac fox. Selective pressure analysis showed that 16 positively selected genes (PSGs) were identified in corsac fox, red fox, and arctic fox. Enrichment analysis of PSGs showed that the LRP11 gene was enriched in several pathways related to the low‐temperature response and might play a key role in response to environmental stimuli of foxes. In addition, several positively selected genes were related to DNA damage repair (ELP2 and CHAF1A), innate immunity (ARRDC4 and S100A12), and the respiratory chain (NDUFA5), and these positively selected genes might play a role in adaptation to harsh wild fox environments. The results of common orthologous gene analysis showed that gene flow or convergent evolution might be an important factor in promoting regional differentiation of foxes. Our study provides a valuable transcriptomic resource for the evolutionary history of the corsac fox and the adaptations to the extreme environments.