Genome Synteny Analysis Research Articles

Characterization, expressional and evolutionary analysis of five fish-specific CCRs (CCR4La, CCR4Lc, CCR12a1, CCR12a2, and CCR12b) in largemouth bass (Micropterus salmoides)

CC chemokine receptors (CCRs), the numbers of the G protein-coupled receptor (GPCR) superfamily, had crucial roles in treating infection, inflammation, and tissue damage by binding to their ligands. In this study, five fish-specific CCRs, namely CCR4La, CCR4Lc, CCR12a1, CCR12a2, and CCR12b, were identified in largemouth bass (Micropterus salmoides). The correction of nomenclatures of these CCRs were confirmed by phylogenetic analysis, structural analysis and genomic synteny analysis. Following 1×106 CFU/mL and 1×107 CFU/mL Edwardsiella piscicida infection, these five CCRs were significantly induced in spleen of largemouth bass, indicating their important roles in the immune response against bacterial infection. Selection pressure analysis revealed that CCR4La, CCR4Lc, CCR12a1, and CCR12a2 underwent negative selection pressure, whereas CCR12b experienced positive selection pressure. Robust selection site detection methods identified that positive selected sites of CCR4La, CCR4Lc, CCR12a1, and CCR12a2 mainly distributed in their extracellular regions, which involved in ligand binding and pathogen interaction. Similarly, the positive selected sites of CCR12b were also located in its extracellular regions. The accuracy of the pressure selected sites were also validated by molecular docking analysis. The potential ligands for these five CCRs were identified by molecular docking analysis, with finding that CCL3 and CCL5 might be the ligands of largemouth bass CCR4La/Lc, and CCL5, CCL8, CCL7, CCL13 and CCL26 might be that of largemouth bass CCR12a1/a2/b. Our results provided basis for elucidating the functions of chemokine-receptor complex in largemouth bass.

Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach.

The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.

Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid

Actinidia arguta, known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such as small and smooth-fruited, rich in beneficial nutrients, rapid softening and tolerant to extremely low temperatures. It contains the most diverse ploidy types, including diploid, tetraploid, hexaploid, octoploid, and decaploid. Here we report a haplotype-resolved tetraploid genome (A. arguta cv. ‘Longcheng No.2’) containing four haplotypes, each with 40,859, 41,377, 39,833 and 39,222 protein-coding genes. We described the phased genome structure, synteny, and evolutionary analyses to identify and date possible WGD events. Ks calculations for both allelic and paralogous genes pairs throughout the assembled haplotypic individuals showed its tetraploidization is estimated to have formed ~ 1.03 Mya following Ad-α event occurred ~ 18.7 Mya. Detailed annotations of NBS-LRRs or CBFs highlight the importance of genetic variations coming about after polyploidization in underpinning ability of immune responses or environmental adaptability. WGCNA analysis of postharvest quality indicators in combination with transcriptome revealed several transcription factors were involved in regulating ripening kiwi berry texture. Taking together, the assembly of an A. arguta tetraploid genome provides valuable resources in deciphering complex genome structure and facilitating functional genomics studies and genetic improvement for kiwifruit and other crops.Graphical

De novo genome assembly and population genomics of a shrub tree Barthea barthei (Hance) krass provide insights into the adaptive color variations.

Flower color is a classic example of an ecologically important trait under selection in plants. Understanding the genetic mechanisms underlying shifts in flower color can provide key insights into ecological speciation. In this study, we investigated the genetic basis of flower color divergence in Barthea barthei, a shrub tree species exhibiting natural variation in flower color. We assembled a high-quality genome assembly for B. barthei with a contig N50 of 2.39 Mb and a scaffold N50 of 16.21 Mb. The assembly was annotated with 46,430 protein-coding genes and 1,560 non-coding RNAs. Genome synteny analysis revealed two recent tetraploidization events in B. barthei, estimated to have occurred at approximately 17 and 63 million years ago. These tetraploidization events resulted in massive duplicated gene content, with over 70% of genes retained in collinear blocks. Gene family members of the core regulators of the MBW complex were significantly expanded in B. barthei compared to Arabidopsis, suggesting that these duplications may have provided raw genetic material for the evolution of novel regulatory interactions and the diversification of anthocyanin pigmentation. Transcriptome profiling of B. barthei flowers revealed differential expression of 9 transcription factors related to anthocyanin biosynthesis between the two ecotypes. Six of these differentially expressed transcription factors were identified as high-confidence candidates for adaptive evolution based on positive selection signals. This study provides insights into the genetic basis of flower color divergence and the evolutionary mechanisms underlying ecological adaptation in plants.

Chromosome-level genome assembly of the kiang (Equus kiang) illuminates genomic basis for its high-altitude adaptation.

The kiang (Equus kiang) can only be observed in the Qinghai-Tibet Plateau (QTP). The kiang displayed excellent athletic performance in the high-altitude environment, which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment. Here, we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology. A total of 324.14 Gb clean data were generated, and the chromosome-level genome with 26 chromosomes (25 + X) and scaffold N50 of 101.77 Mb was obtained for the kiang. The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species. Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya. The expanded gene families were mainly related to the hypoxia response, metabolism, and immunity. The kiang suffered a significant loss of olfaction-related genes, which might indicate decreased olfactory sensibility. Positively selected genes (PSGs) detected in the kiang were mainly associated with hypoxia response. Especially, there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway, which may play an important role in the high-altitude adaptation of the kiang. Moreover, structure variations in the kiang genome were also identified, which possibly contributed to the high-altitude adaptation of the kiang. Comparative analysis revealed a lot of species-specific insertions and deletions in the kiang genome, such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region, respectively, possibly affecting the expression and regulation of hypoxia-related downstream pathways. This study provided valuable genomic resources, and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.

Central regulation of reproduction in amphibians.

This review article includes a literature review of synteny analysis of the amphibian gonadotropin-releasing hormone (GnRH) genes, the distribution of GnRH 1 and GnRH2 neurons in the central nervous system of amphibians, the function and regulation of hypophysiotropic GnRH1, and the function of GnRH1 in amphibian reproductive behaviors. It is generally accepted that GnRH is the key regulator of the hypothalamic-pituitary-gonadal axis. Three independent GnRH genes, GnRH1, GnRH2, and GnRH3, have been identified in vertebrates. Previous genome synteny analyses suggest that there are likely just two genes, gnrh1 and gnrh2, in amphibians. In three groups of amphibians: Anura, Urodela, and Gymnophiona, the distributions of GnRH1 and GnRH2 neurons in the central nervous system have also been previously reported. Moreover, these neuronal networks were determined to be structurally independent in all species examined. The somata of GnRH1 neurons are located in the terminal nerve, medial septum (MS), and preoptic area (POA), and some GnRH1 neurons in the MS and POA project into the median eminence. In contrast, the somata of GnRH2 neurons are located in the midbrain tegmentum. In amphibians, GnRH1 neurons originate from the embryonic olfactory placode, while GnRH2 neurons originate from the midbrain. The characterization and feedback regulation mechanisms of hypophysiotropic GnRH1 neurons in amphibians, the involvement of GnRH1 in amphibian reproductive behavior, and its possible mechanism of action should be elucidated in future.

GENOME-WIDE ANALYSES OF CORE REGULATORY MODULE SHATTERING CASCADE GENES IN CANOLA (BRASSICA NAPUS L.)

Premature seed shattering in canola causes massive losses in yield by up to 50% in adverse climatic conditions. In the model plant Arabidopsis thaliana, which belongs to the same family as canola, the Brassicaceae, eight genes participate in a shattering cascade. Phylogenetic reconstruction, syntenic relationships, genomics loci, promoter sequences, and identification of transcription factor-binding sites (TFBSs) faced shattering cascade genes’ analysis. Among these, three genes, SHATTERPROOF1, SHATTERPROOF2, and FRUITFUL (SHP1, SHP2, FUL), belonged to a MADS-box family implicated in fruit dehiscence zone and valve margin constitute a core regulatory module. But, in Brassica, the exact number of genes involved in shattering remained obscure. Grouping BnSHP1-N, BnSHP2-N, and BnFUL-N into their respective clades was according to phylogenetic reconstruction of core regulatory modules (SHP1, SHP2, and FUL) and from other species homologs. The eight shattering cascade genes showed no conservation, indicating their involvement in crushing through separate pathways. The increased number of homologs/paralogs in Brassica was due to occurrences of genome duplication or a triplication event during evolution. Exonization and intronization could be responsible for a variable number and size of the exons and introns in gene structures. Comparative genome synteny analysis of SHP1, SHP2, and FUL revealed correlation and evolutionary insights into gene region relationships in all Brassicaceae. Study results provided basic information on cloning, phylogenetic reconstruction, genomics loci, and identifying transcription factor-binding sites (TFBSs) of core regulatory module genes that might be helpful for developing shattering-resistant genome-edited plants to prevent future yield losses in canola.

Toll-like Receptor 3 in the Hybrid Yellow Catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂): Protein Structure, Evolution and Immune Response to Exogenous Aeromonas hydrophila and Poly (I:C) Stimuli.

As a major mediator of cellular response to viral infection in mammals, Toll-like receptor 3 (TLR3) was proved to respond to double-stranded RNA (dsRNA). However, the molecular mechanism by which TLR3 functions in the viral infection response in teleosts remains to be investigated. In this study, the Toll-like receptor 3 gene of the hybrid yellow catfish was identified and characterized by comparative genomics. Furthermore, multiple sequence alignment, genomic synteny and phylogenetic analysis suggested that the homologous TLR3 genes were unique to teleosts. Gene structure analysis showed that five exons and four introns were common components of TLR3s in the 12 examined species, and interestingly the third exon in teleosts was the same length of 194 bp. Genomic synteny analysis indicated that TLR3s were highly conserved in various teleosts, with similar organizations of gene arrangement. De novo predictions showed that TLR3s were horseshoe-shaped in multiple taxa except for avian (with a round-shaped structure). Phylogenetic topology showed that the evolution of TLR3 was consistent with the evolution of the studied species. Selection analysis showed that the evolution rates of TLR3 proteins were usually higher than those of TLR3-TIR domains, indicating that the latter were more conserved. Tissue distribution analysis showed that TLR3s were widely distributed in the 12 tested tissues, with the highest transcriptions in liver and intestine. In addition, the transcription levels of TLR3 were significantly increased in immune-related tissues after infection of exogenous Aeromonas hydrophila and poly (I:C). Molecular docking showed that TLR3 in teleosts forms a complex with poly (I:C). In summary, our present results suggest that TLR3 is a pattern recognition receptor (PRR) gene in the immune response to pathogen infections in hybrid yellow catfish.

Genome-Wide Identification of MIKCc-Type MADS-Box Family Gene and Floral Organ Transcriptome Characterization in Ma Bamboo (Dendrocalamus latiflorus Munro).

Most bamboos die after flowering, and the molecular mechanisms responsible for flowering is poorly understood. The MIKCc-type MADS-box family gene is involved in the flowering process. To explore the mechanism of the MIKCc-type MADS-box gene and phytohormone regulation in the flowering of Dendrocalamus latiflorus Munro (D. latiflorus), characterized by extremely rapid growth and widely cultivated woody bamboo, we initially did a genome-wide analysis of the MIKCc-type MADS-box gene in D. latiflorus. In the meantime, transcriptome analysis was performed using the floral organs. A total of 170 MIKCc-Type MADS-Box genes were identified and divided into 15 categories. The cis-acting element analysis in promoters regions revealed that MIKC-type MADS-box family genes were associated with hormones, including auxin, abscisic acid (ABA), gibberellin (GA) and jasmonic acid (JA), which was found at 79, 476, 96, 486 sites and cover 61, 103, 73, 128 genes. Genome synteny analysis showed subgenome AA and BB were better than CC and obtained 49, 40, 39 synteny genes compared with Oryza sativa (O. sativa). In transcriptome analysis of floral organs, the enriched pathway from DEGs included circadian, vernalization and gibberellin pathways associated with the flowering process. We found that the jasmonic acid synthesis gene is highly expressed in the pistil, which may be the cause of Ma bamboo pollen abortion. The expression profile showed that most MIKC-type MADS-box genes exhibited high expression in flower organs. The consequences of this study will provide insight into the irregular flowering and low pollen counts of Ma bamboo.

Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains.

Recurrent epidemics of cholera denote robust adaptive mechanisms of Vibrio cholerae for ecological shifting and persistence despite variable stress conditions. Tracking the evolution of pathobiological traits requires comparative genomic studies of isolates from endemic areas. Here, we investigated the genetic differentiation among V. cholerae clinical and environmental isolates by highlighting the genomic divergence associated with gene decay, genome plasticity, and the acquisition of virulence and adaptive traits. The clinical isolates showed high phylogenetic relatedness due to a higher frequency of shared orthologs and fewer gene variants in contrast to the evolutionarily divergent environmental strains. Divergence of the environmental isolates is linked to extensive genomic rearrangements in regions containing mobile genetic elements resulting in numerous breakpoints, relocations, and insertions coupled with the loss of virulence determinants acf, zot, tcp, and ctx in the genomic islands. Also, four isolates possessed the CRISPR-Cas systems with spacers specific for Vibrio phages and plasmids. Genome synteny and homology analysis of the CRISPR-Cas systems suggest horizontal acquisition. The marked differences in the distribution of other phage and plasmid defense systems such as Zorya, DdmABC, DdmDE, and type-I Restriction Modification systems among the isolates indicated a higher propensity for plasmid or phage disseminated traits in the environmental isolates. Our results reveal that V. cholerae strains undergo extensive genomic rearrangements coupled with gene acquisition, reflecting their adaptation during ecological shifts and pathogenicity.

Molecular evolution of the BRINP and ASTN genes and expression profles in response to pathogens and spinal cord injury repair in lamprey (Lethenteron reissneri)

Bone morphogenic protein/retinoic acid inducible neural-specific proteins (BRINPs) and astrotactins (ASTNs) are two members of membrane attack complex/perforin-like (MACPF) superfamily proteins that present high expression in the growing and mature vertebrate neurons. Lamprey has a unique evolutionary status as a representative of the oldest jawless vertebrates, making it an ideal animal model for understanding vertebrate evolution. The evolutionary origins of BRINPs and ASTNs genes in vertebrates, however, have not been shown in lampreys. Here, BRINP and ASTN genes were found in lamprey genomes and the evolutionary relationships of them were investigated by phylogenetic analysis. Protein domains, motifs, genetic structure, and crystal structure analysis revealed that the features of BRINP and ASTN appear to be conserved in vertebrates. Genomic synteny analysis indicated that lamprey BRINP and ASTN neighbor genes differed dramatically from jawed vertebrate. Real-time quantitative results illustrated that the BRINP and ASTN genes family might take part in immune defence and spinal cord injury repair. This study not only enriches a better understanding of the evolution of the BRINP and ASTN genes but also offers a foundation for exploring their roles in the development of the vertebrate central nervous system (CNS).

Genome-wide identification, evolutionary analysis, and antimicrobial activity prediction of CC chemokines in allotetraploid common carp, Cyprinus carpio

Chemokines are a group of secreted small molecules which are essential for cell migration in physiological and pathological conditions by binding to specific chemokine receptors. They are structurally classified into five groups, namely CXC, CC, CX3C, XC and CX. CC chemokine group is the largest one among them. In this study, we identified and characterized 61 CC chemokines from allotetraploid common carp (Cyprinus carpio). The sequence analyses showed that the majority of CC chemokines had an N-terminal signal peptide, and an SCY domain, and all CC chemokines were located in the extracellular region. Phylogenetic, evolutionary and syntenic analyses confirmed that CC chemokines were annotated as 11 different types (CCL19, CCL20, CCL25, CCL27, CCL32, CCL33, CCL34, CCL35, CCL36, CCL39, and CCL44), which exhibited unique gene arrangement pattern and chromosomal location respectively. Furthermore, genome synteny analyses between common carp and four representative teleost species indicated expansion of common carp CC chemokines resulted from the whole genome duplication (WGD) event. Additionally, the continuous evolution of gene CCL25s in teleost afforded a novel viewpoint to explain the WGD event in teleost. Then, we predicted the three-dimensional structures and probable function regions of common carp CC chemokines. All the CC chemokines core structures were constituted of an N-loop, a three-stranded β-sheet, and a C-terminal helix. Finally, 43 CC chemokines were predicted to have probable general antimicrobial activity. Their tertiary structures, cationic and amphiphilic physicochemical property supported the viewpoint. To verify the prediction, six recombinant CCL19s proteins were prepared and the antibacterial activity against Escherichia coli and Aeromonas hydrophila were verified. The results supported our prediction that rCCL19a.1s (rCCL19a.1_a, rCCL19a.1_b) and rCCL19bs (rCCL19b_a, rCCL19b_b), especially rCCL19bs, exhibited extremely significant inhibition to the growth of both E. coli and A. hydrophila. On the contrary, two rCCL19a.2s had no significant inhibitory effect. These studies suggested that CC chemokines were essential in immune system evolution and not monofunctional during pathogen infection.

Pseudo-Chromosomal Genome Assembly in Combination with Comprehensive Transcriptome Analysis in Agaricus bisporus Strain KMCC00540 Reveals Mechanical Stimulus Responsive Genes Associated with Browning Effect.

Agaricus bisporus is one of the world’s most popular edible mushrooms, including in South Korea. We performed de novo genome assembly with a South Korean white-colored cultivar of A. bisporus, KMCC00540. After generating a scaffold-level genomic sequence, we inferred chromosome-level assembly by genomic synteny analysis with the representative A. bisporus strains H97 and H39. The KMCC00540 genome had 13 pseudochromosomes comprising 33,030,236 bp mostly covering both strains. A comparative genomic analysis with cultivar H97 indicated that most genomic regions and annotated proteins were shared (over 90%), ensuring that our cultivar could be used as a representative genome. However, A. bisporus suffers from browning even from only a slight mechanical stimulus during transportation, which significantly lowers its commercial value. To identify which genes respond to a mechanical stimulus that induces browning, we performed a time-course transcriptome analysis based on the de novo assembled genome. Mechanical stimulus induces up-regulation in long fatty acid ligase activity-related genes, as well as melanin biosynthesis genes, especially at early time points. In summary, we assembled the chromosome-level genomic information on a Korean strain of A. bisporus and identified which genes respond to a mechanical stimulus, which provided key hints for improving the post-harvest biological control of A. bisporus.

Population genomics of the grapevine pathogen Eutypa lata reveals evidence for population expansion and intraspecific differences in secondary metabolite gene clusters.

Eutypa dieback of grapevine is an important disease caused by the generalist Ascomycete fungus Eutypa lata. Despite the relevance of this species to the global wine industry, its genomic diversity remains unknown, with only a single publicly available genome assembly. Whole-genome sequencing and comparative genomics was performed on forty Australian E. lata isolates to understand the genome evolution, adaptation, population size and structure of these isolates. Phylogenetic and linkage disequilibrium decay analyses provided evidence of extensive gene flow through sexual recombination between isolates obtained from different geographic locations and hosts. Investigation of the genetic diversity of these isolates suggested rapid population expansion, likely as a consequence of the recent growth of the Australian wine industry. Genomic regions affected by selective sweeps were shown to be enriched for genes associated with secondary metabolite clusters and included genes encoding proteins with a role in nutrient acquisition, degradation of host cell wall and metal and drug resistance, suggesting recent adaptation to both abiotic factors and potentially host genotypes. Genome synteny analysis using long-read genome assemblies showed significant intraspecific genomic plasticity with extensive chromosomal rearrangements impacting the secondary metabolite production potential of this species. Finally, k-mer based GWAS analysis identified a potential locus associated with mycelia recovery in canes of Vitis vinifera that will require further investigations.

Identification and expression analysis of the PtGATL genes under different nitrogen and carbon dioxide treatments in Populus trichocarpa.

The online version contains supplementary material available at 10.1007/s13205-022-03129-y.

Molecular evolution of hatching enzymes and their paralogous genes in vertebrates

BackgroundHatching is identified as one of the most important events in the reproduction of oviparous vertebrates. The genes for hatching enzymes, which are vital in the hatching process, are conserved among vertebrates. However, especially in teleost, it is difficult to trace their molecular evolution in detail due to the presence of other C6astacins, which are the subfamily to which the genes for hatching enzymes belong and are highly diverged. In particular, the hatching enzyme genes are diversified with frequent genome translocations due to retrocopy.ResultsIn this study, we took advantage of the rapid expansion of whole-genome data in recent years to examine the molecular evolutionary process of these genes in vertebrates. The phylogenetic analysis and the genomic synteny analysis revealed C6astacin genes other than the hatching enzyme genes, which was previously considered to be retained only in teleosts, was also retained in the genomes of basal ray-finned fishes, coelacanths, and cartilaginous fishes. These results suggest that the common ancestor of these genes can be traced back to at least the common ancestor of the Gnathostomata. Moreover, we also found that many of the C6astacin genes underwent multiple gene duplications during vertebrate evolution, and the results of gene expression analysis in frogs implied that genes derived from hatching enzyme genes underwent neo-functionalization.ConclusionsIn this study, we describe in detail the molecular evolution of the C6astacin gene in vertebrates, which has not been summarized previously. The results revealed the presence of the previously unknown C6astacin gene in the basal-lineage of jawed vertebrates and large-scale gene duplication of hatching enzyme genes in amphibians. The comprehensive investigation reported in this study will be an important basis for studying the molecular evolution of the vertebrate C6astacin genes, hatching enzyme, and its paralogous genes and for identifying these genes without the need for gene expression and functional analysis.

Global Analysis of the WOX Transcription Factor Gene Family in Populus × xiaohei T. S. Hwang et Liang Reveals Their Stress−Responsive Patterns

The WUSCHEL−related homeobox (WOX) family is a group of plant−specific transcription factors that play important regulatory roles in embryo formation, stem cell stability, and organogenesis. To date, there are few studies on the molecular mechanisms involved in this family of genes in response to stress. Thus, in this study, eight WOX genes were obtained from an endemic Chinese resilient tree species, Populus × xiaohei T. S. Hwang et Liang. Bioinformatic analysis showed that the WOX genes all contained a conserved structural domain consisting of 60 amino acids, with some differences in physicochemical properties. Phylogenetic analysis revealed that WOX members were divided into three evolutionary clades, with four, one, and three members in the ancient, intermediate, and modern evolutionary clades, respectively. The conserved structural domain species as well as the organization and gene structure of WOX genes within the same subfamily were highly uniform. Chromosomal distribution and genome synteny analyses revealed seven segmental−duplicated gene pairs among the PsnWOX gene family that were mainly under purifying selection conditions. Semi−quantitative interpretation (SQ−PCR) analysis showed that the WOX gene was differentially expressed in different tissues, and it was hypothesized that the functions performed by different members were diverse. The family members were strongly and differentially expressed under CdCl2, NaCl, NaHCO3, and PEG treatments, suggesting that WOX genes function in various aspects of abiotic stress defense responses. These results provide a theoretical basis for investigating the morphogenetic effects and abiotic stress responses of this gene family in woody plants.

Comparative genomic analysis reveals new evidence of genus boundary for family Iridoviridae and explores qualified hallmark genes

Members of the family Iridoviridae (iridovirids) are globally distributed and trigger adverse economic and ecological impacts on aquaculture and wildlife. Iridovirids taxonomy has previously been studied based on a limited number of genomes, but this is not suitable for the current and future virological studies as more iridovirids are emerging. In our study, 57 representative iridovirids genomes were selected from a total of 179 whole genomes available on NCBI. Then 18 core genes were screened out for members of the family Iridoviridae. Average amino acid sequence identity (AAI) analysis indicated that a cut-off value of 70% is more suitable for the current iridovirids genome database than ICTV-defined 50% threshold to better clarify viral genus boundaries. In addition, more subgroups were divided at genus level with the AAI threshold of 70%. This observation was further confirmed by genomic synteny analysis, codon usage preference analysis, genome GC content and length analysis, and phylogenic analysis. According to the pairwise comparison analysis of core genes, 9 hallmark genes were screened out to conduct preliminary identification and investigation at the genus level of iridovirids in a more convenient and economical manner.

Identification, molecular evolution, and expression analysis of the transcription factor Smad gene family in lamprey

Transcription factor small mothers against decapentaplegic (Smad) family SMAD proteins are the essential intracellular signal mediators and transcription factors for transforming growth factor β (TGF-β) signal transduction pathway, which usually exert pleiotropic actions on cell physiology, including immune response, cell migration and differentiation. In this study, the Smad family was identified in the most primitive vertebrates through the investigation of the transcriptome data of lampreys. The topology of phylogenetic tree showed that the four Smads (Smad1, Smad3, Smad4 and Smad6) in lampreys were subdivided into four different groups. Meanwhile, homology analysis indicated that most Smads were conserved with typical Mad Homology (MH) 1 and MH2 domains. In addition, Lethenteron reissneri Smads (Lr-Smads) adopted general Smads folding structure and had high tertiary structural similarity with human Smads (H-Smads). Genomic synteny analysis revealed that the large-scale duplication blocks were not found in lamprey genome and neighbor genes of lamprey Smads presented dramatic differences compared with jawed vertebrates. Importantly, quantitative real-time PCR analysis demonstrated that Smads were widely expressed in lamprey, and the expression level of Lr-Smads mRNA was up-regulated with different pathogenic stimulations. Moreover, depending on the weighted gene co-expression network analysis (WGCNA), four Lr-Smads were identified as two meaningful modules (green and gray). The functional analysis of these two modules showed that they might have a correlation with ployI:C. And these genes presented strong positive correlation during the immune response from the results of Pearson's correlation analysis. In conclusion, our results would not only enrich the information of Smad family in jawless vertebrates, but also lay the foundation for immunity in further study.

Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)

Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. In our results, a total of 27 SOX (high-mobility group HMG-box) domain genes were identified in the C. carp genome. The full length sequences of SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative proteins series from 307 to 509 amino acids and all gene having exon number expect SOX9 and SOX13. All the SOX proteins contained at least one conserved DNA-binding HMG-box domain and two (SOX7 and SOX18) were found C terminal. The Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %, average in biological regulation 45.188 %, biosynthetic process (19.992 %), regulation of cellular process 39.68, 45.508 % organic substance metabolic process, multicellular organismal process 23.23 %,developmental process 21.74 %, system development 16.59 %, gene expression 16.05 % and 14.337 % of RNA metabolic process. Chromosomal location and syntanic analysis show all SOX gene are located on different chromosomes and apparently does not fallow the unique pattern. The maximum linkage of chromosome is (2) on Unplaced Scaffold region. Finally, our results provide important genomic suggestion for upcoming studies of biochemical, physiological, and phylogenetic understanding on SOX genes among teleost.