Sequence Divergence Research Articles

Taxonomy and multigene phylogeny of Pseudohydnum (Auriculariales, Basidiomycota)

Taxonomy of Pseudohydnum gelatinosum and its sister taxa is revised via morphological data and a four-gene dataset (ITS, nc LSU rDNA, TEF1, RPB1). Identity of P. gelatinosum and Tremellodon pusillus is re-established based on newly collected and sequenced material from their type localities. Pseudohydnum alienum from Europe; P. umbrosum from temperate East Asia; P. cystidiatum, P. meridianum, and P. placibile from Vietnam; and P. omnipavum from North America are described as new to science; P. translucens and P. brunneiceps from East Asia are redescribed. Most Pseudohydnum collections from North America belong to P. gelatinosum ssp. pusillum. A significant divergence of TEF1 sequences in P. gelatinosum is discussed.

Complete Chloroplast Genome of Bamboo Species Pleioblastus ovatoauritus and Comparative Analysis of Pleioblastus from China and Japan

Pleioblastus ovatoauritus T.H.Wen ex W.Y.Zhang is bamboo species published in 2018, originated from and existing in southeastern China. The chloroplast genome of Pl. ovatoauritus was obtained using a high-throughput sequencing platform. The chloroplast genome is up to 139,708 bp in length and displays a typical quadripartite structure with one large single-copy region, one small single-copy region, and two inverted repeat regions. There are 82 protein-coding genes, 8 rRNA genes, and 39 tRNA genes in the plastome genome. However, the interspecific relationship of Pleioblastus species originated from China and Japan has not been revealed explicitly. To understand their relationship, data from four Chinese species and four Japanese species were selected to investigate the distinctions between their genome structures, codon usage patterns, and SSR sites. We moved forward to examine the sequence divergence and polymorphic sites between the eight species. Phylogenetic trees were then plotted using the maximum likelihood method based on different parts of the sequences. Obvious difference found in the JLB boundary and a split in the phylograms contributed to our decision to split Pleioblastus species of China and Japan into different clades. Moreover, taxonomy using the subgenera concept in Flora Reipublicae Popularis Sinicae proved untenable. Nine SSR primers for Pleioblastus genus were then developed from cp genomes, aimed at facilitating identification and germplasm investigation.

Two new spotted species of the Cyrtodactylus (Geckoella) collegalensis (Beddome, 1870) complex from the south-eastern coast of India (Reptilia: Squamata)

We describe two new spotted species of ground-dwelling gecko of the genus Cyrtodactylus (Geckoella) from southeastern India in an integrative taxonomic framework. The new species are recovered as sister taxa within the C. collegalensis species complex, with 13.0–16.7% uncorrected mitochondrial sequence divergence from the other eight members of the C. collegalensis complex and 10.4% from one another. The new species are morphologically diagnosed by a spotted dorsal pattern of four pairs of spots (occasionally fused into figure 8-shaped markings) from the banded species C. aravindi, C. speciosus, C. rishivalleyensis and C. yakhuna; and from the spotted species with three or fewer pairs of spots in C. collegalensis and C. srilekhae; and from C. chengodumalaensis by the absence of any enlarged dorsal scales and from C. varadgirii by the absence of a patch of enlarged roughly hexagonal scales on the canthus rostralis and beneath the angle of the lower jaw. The two new species can only be differentiated from each other based on slight differences in body size, relative body width and other statistically significant, size-corrected morphometric characters. These are among the first endemic lizards from Tropical Dry Evergreen habitats along the southeast coast of India.

Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

BackgroundThe Western mosquitofish, Gambusia affinis, is a model for sex chromosome organization and evolution of female heterogamety. We previously identified a G. affinis female-specific marker, orthologous to the aminomethyl transferase (amt) gene of the related platyfish (Xiphophorus maculatus). Here, we have analyzed the structure and differentiation of the G. affinis W-chromosome, using a cytogenomics and bioinformatics approach.ResultsThe long arm of the G. affinis W-chromosome (Wq) is highly enriched in dispersed repetitive sequences, but neither heterochromatic nor epigenetically silenced by hypermethylation. In line with this, Wq sequences are highly transcribed, including an active nucleolus organizing region (NOR). Female-specific SNPs and evolutionary young transposable elements were highly enriched and dispersed along the W-chromosome long arm, suggesting constrained recombination. Wq copy number expanded elements also include female-specific transcribed sequences from the amt locus with homology to TE. Collectively, the G. affinis W-chromosome is actively differentiating by sex-specific copy number expansion of transcribed TE-related elements, but not (yet) by extensive sequence divergence or gene decay.ConclusionsThe G. affinis W-chromosome exhibits characteristic genomic properties of an evolutionary young sex chromosome. Strikingly, the observed sex-specific changes in the genomic landscape are confined to the W long arm, which is separated from the rest of the W-chromosome by a neocentromere acquired during sex chromosome evolution and may thus have become functionally insulated. In contrast, W short arm sequences were apparently shielded from repeat-driven differentiation, retained Z-chromosome like genomic features, and may have preserved pseudo-autosomal properties.

Genomic variability correlates with biofilm phenotypes in multidrug resistant clinical isolates of Pseudomonas aeruginosa

The multifactorial nature of Pseudomonas aeruginosa biofilm development and genomic variabilities implicates its resistance to conventional antimicrobials and virulence. Therefore, genetic determinants need to be extensively studied to block the early steps of biofilm or already formed biofilms. In this study, a total of 20 multidrug resistant (MDR) clinical P. aeruginosa isolates were evaluated for their biofilm forming abilities and related genes. Of the isolates tested, all of them showed surface attachment tendencies in nutrient limiting conditions, and classified as strong (SBF = 45%), moderate (MBF = 30%) and weak (WBF = 25%) biofilm formers. Complete genome sequencing of representative strong (DMC-27b), moderate (DMC-20c) and weak biofilm former (DMC-30b) isolates was performed. Analysis of biofilm related genes in the sequenced genomes revealed that, 80 of the 88 biofilm related genes possess 98–100% sequence identity to the reference PAO1 strain. Complete and partial sequence data of LecB proteins from tested isolates indicate that isolates containing PA14-like LecB sequences produced strong biofilms. All of the 7 pel operon protein coding genes in weak biofilm former isolate 30b showed significant nucleotide sequence variation with other tested isolates, and their corresponding proteins are 99% identical with the pel operon proteins of PA7. Bioinformatics analyses identified divergent sequence and structural features that separate PA7 like pel operon proteins from reference PAO1-like pel operon. Congo red and pellicle forming assays revealed that the sequence and structure variations may have interfered with the Pel production pathway and resulted in impaired Pel production in isolate 30b that has a PA7 like pel operon. Expression analysis also showed that both pelB and lecB genes were about 5 to 6 folds upregulated after 24 h in SBF 27b in comparison with WBF 30b. Our findings indicate significant genomic divergence in biofilm related genes of P. aeruginosa strains that affect their biofilm phenotypes.

Deciphering Divergent Trypanosomatid Nuclear Complexes by Analyzing Interactomic Datasets with AlphaFold2 and Genetic Approaches.

Acetylation signaling pathways in trypanosomatids, a group of early branching organisms, are poorly understood due to highly divergent protein sequences. To overcome this challenge, we used interactomic datasets and AlphaFold2 (AF2)-multimer to predict direct interactions and validated them using yeast two and three-hybrid assays. We focused on MORF4 related gene (MRG) domain-containing proteins and their interactions, typically found in histone acetyltransferase/deacetylase complexes. The results identified a structurally conserved complex, TcTINTIN, which is orthologous to human and yeast trimer independent of NuA4 for transcription interaction (TINTIN) complexes; and another trimeric complex involving an MRG domain, only seen in trypanosomatids. The identification of a key component of TcTINTIN, TcMRGBP, would not have been possible through traditional homology-based methods. We also conducted molecular dynamics simulations, revealing a conformational change that potentially affects its affinity for TcBDF6. The study also revealed a novel way in which an MRG domain participates in simultaneous interactions with two MRG binding proteins binding two different surfaces, a phenomenon not previously reported. Overall, this study demonstrates the potential of using AF2-processed interactomic datasets to identify protein complexes in deeply branched eukaryotes, which can be challenging to study based on sequence similarity. The findings provide new insights into the acetylation signaling pathways in trypanosomatids, specifically highlighting the importance of MRG domain-containing proteins in forming complexes, which may have important implications for understanding the biology of these organisms and developing new therapeutics. On the other hand, our validation of AF2 models for the determination of multiprotein complexes illuminates the power of using such artificial intelligence-derived tools in the future development of biology.

The Complete Chloroplast Genomes of Blepharoglossum elegans and B. grossum and Comparative Analysis with Related Species (Orchidaceae, Malaxideae).

Blepharoglossum is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of Blepharoglossum has been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of two Blepharoglossum species, Blepharoglossum elegans (Lindl.) L. Li and Blepharoglossum grossum (Rchb.f.) L. Li. These cp genomes of Blepharoglossum share the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, with ycf1, clpP, and trnK-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namely rps16-trnQ-UUG, trnS-GCU-trnG-GCC, rpoB-trnC-GCA, trnE-UUC-trnT-GGU, trnF-GAA-trnV-UAC, atpB-rbcL, petA-psbJ, psbE-petL, psbB-psbT, trnN-GUU-rpl32, trnV-GAC-rps7, and rps7-trnL-CAA, and five coding regions, including matK, and rpoC2, ycf1, and two ycf2 genes. Phylogenetic analysis indicated that Blepharoglossum and Oberonia form a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades.

Genome-Wide Identification and Expression Analysis of Calmodulin (CaM) and Calmodulin-Like (CML) Genes in the Brown Algae Saccharina japonica.

Calmodulins (CaMs) and Calmodulin-like proteins (CMLs) are vital in plant growth, development, and stress responses. However, CaMs and CMLs have not been fully identified and characterized in brown algae, which has been evolving independently of the well-studied green plant lineage. In this study, whole-genome searches revealed one SjCaM and eight SjCMLs in Saccharina japonica, and one EsCaM and eleven EsCMLs in Ectocarpus sp. SjCaM and EsCaM encoded identical protein products and shared 88.59-89.93% amino acid identities with Arabidopsis thaliana AtCaMs, thereby indicating that brown algae CaMs retained a similar Ca2+ sensors function as in plants. The phylogenetic and gene structure analysis results showed that there was significant divergence in the gene sequences among brown algae CMLs. Furthermore, evolutionary analysis indicated that the function of brown alga CMLs was relatively conserved, which may be related to the fact that brown algae do not need to face complex environments like terrestrial plants. Regulatory elements prediction and the expression analysis revealed the probable functioning of SjCaM/CML genes in gametophyte development and the stress response in S. japonica. In addition, the SjCaM/SjCMLs interacting proteins and chemicals were preliminarily predicted, suggesting that SjCaM/SjCMLs might play putative roles in Ca2+/CaM-mediated growth and development processes and stimulus responses. Therefore, these results will facilitate our understanding of the evolution of brown algae CaMs/CMLs and the functional identification of SjCaM/SjCMLs.

Transcriptional misexpression in hybrids between species linked by gene flow is associated with patterns of sequence divergence.

The extent to which hybridization disrupts a gene's pattern of expression likely governs its propensity for introgression, while its extent of molecular divergence can itself underlie such disruption. Together, these phenomena shape the landscape of sequence and transcriptional divergence across the genome as species diverge. To understand this process, we characterize gene expression inheritance, regulatory divergence, and molecular divergence in the reproductive transcriptomes of species linked by gene flow: the fruit flies Anastrepha fraterculus and A. obliqua, which show evidence of gene flow despite clear evolutionary divergence. We find that their transcriptional patterns are a mosaic between those typically observed within and between allopatric species. Transcripts showing transgressive expression in hybrids or cis-regulatory divergence between species are associated with greater sequence divergence. This may reflect pleiotropic constraints that make them resistant to gene flow or they may be more likely to experience divergent selection. While these more divergent gene classes are likely to be important contributors to species differences, they are relatively rare. Instead, most differentially regulated transcripts, including those linked to reproduction, show high degrees of dominance in hybrids and trans-regulated divergence between species, suggesting widespread genetic compatibility that potentially allowed for introgression. These findings provide insights into how postzygotic isolating mechanisms might evolve in the presence of gene flow: regions showing cis-regulatory divergence or transgressive expression contribute to reproductive isolation, while regions with dominant expression and trans-regulatory divergence allow for introgression. These patterns create a genomic mosaic of transcriptional regulation that is tied to sequence divergence.

Unbiased analyses of ITS folding motifs in a taxonomically confusing lineage: Anagnostidinema visiae sp. nov. (CYANOBACTERIA).

Cyanobacteria are diverse prokaryotic, photosynthetic organisms present in nearly every known ecosystem. Recent investigations around the world have recovered vast amounts of novel biodiversity in seldom sampled habitats. One phylogenetically significant character, the secondary folding structures of the 16S-23S ITS rDNA region, has allowed an unprecedented capacity to erect new species. However, two questions arise: is this feature as informative as is proposed, and how do we best employ these features? Submerged sinkholes with oxygen-poor, sulfur-rich ground water in Lake Huron (USA) contain microbial mats dominated by both oxygenic and anoxygenic cyanobacteria. We sought to document some of this unique cyanobacterial diversity. Using culture-based investigations, we recovered 45 strains, of which 23 were analyzed employing 16S-23S rDNA sequences, ITS folding patterns, ecology, and morphology. With scant morphological discontinuities and nebulous 16S rDNA gene sequence divergence, ITS folding patterns were effective at articulating cryptic biodiversity. However, we would have missed these features had we not folded all the available motifs from the strains, including those with highly similar 16S rDNA gene sequences. If we had relied solely on morphological or 16S rDNA gene data, then we might well have missed the diversity of Anagnostidinema. Thus, in order to avoid conformation basis, which is potentially common when employing ITS structures, we advocate clustering strains based on ITS rDNA region patterns independently and comparing them back to 16S rDNA gene phylogenies. Using a total evidence approach, we erected a new taxon according to the International Code of Nomenclature for Algae, Fungi, and Plants: Anagnostidinema visiae.

Cryptosporidium equi n. sp. (Apicomplexa: Cryptosporidiidae): Biological and genetic characterisations

The horse genotype is one of three common Cryptosporidium spp. in equine animals and has been identified in some human cases. The species status of Cryptosporidium horse genotype remains unclear due to the lack of extensive morphological, biological, and genetic data. In the present study, we have conducted biological and whole genome sequence analyses of an isolate of the genotype from hedgehogs and proposed to name it Cryptosporidium equi n. sp. to reflect its common occurrence in equine animals. Oocysts of C. equi measured 5.12 ± 0.36 μm × 4.46 ± 0.21 μm with a shape index of 1.15 ± 0.08 (n = 50). Cryptosporidium equi was infectious to 3-week-old four-toed hedgehogs (Atelerix albiventris) and mice, with a prepatent period of 2–9 days and a patent period of 30–40 days in hedgehogs. It was not infectious to rats and rabbits. Phylogenetic analyses of small subunit rRNA, 70 kDa heat shock protein, actin, 60 kDa glycoprotein and 100 other orthologous genes revealed that C. equi is genetically distinct from other known Cryptosporidium species and genotypes. The sequence identity between C. equi and Cryptosporidium parvum genomes is 97.9%. Compared with C. parvum, C. equi has lost two MEDLE genes and one insulinase-like protease gene and gained one SKSR gene. In addition, 60 genes have highly divergent sequences (sequence differences ≥ 5.0%), including those encoding mucin-like glycoproteins, insulinase-like peptidases, and MEDLE and SKSR proteins. The genetic uniqueness of C. equi supports its increasing host range and the naming of it as a valid Cryptosporidium species. This is the first known use of whole genome sequence data in delineating new Cryptosporidium species.

Diversity of gut commensal flagellins results in distinct intestinal epithelial cell immune responses

Abstract Flagellins from bacteria in the Lachnospiraceae family are immunodominant antigens in inflammatory bowel disease. Flagellin is the basic unit of flagella which is used for bacterial motility and is recognized by toll-like receptor 5 (TLR5). Due to the diversity in flagellated organisms that reside in proximity to the intestinal epithelium, we asked whether this resulted in distinct interactions between commensal flagellins and the immune system. Analysis of over 200 flagellins, primarily from Lachnospiraceae organisms, revealed a divergence in peptide sequences in specific non-conserved regions of the D0 domain that broadly separate the flagellins examined into 2 clusters which we refer to as Group 1 and Group 2 flagellins. We stimulated HEK-Blue mTLR5 cells and murine intestinal epithelial cells (IECs) with selected Group 1 or Group 2 flagellins to assess TLR5 activity and IEC production of lipocalin-2 (Lcn-2) - a biomarker of inflammation - respectively. Group 2 flagellin strongly activated TLR5 signaling in the mTLR5 HEK cell line, even more so than Salmonella typhimurium (S. typhi) flagellin. Conversely, cells stimulated with the Group 1 flagellin exhibited significantly reduced TLR5 signaling relative to both Group 2 and S. typhi flagellins. While IEC stimulation with Group 1 flagellin resulted in undetectable Lcn-2, stimulation with Group 2 flagellin led to robust Lcn-2 production; more so than stimulation with S. typhi flagellin. These findings demonstrate that flagellins of commensal bacteria elicit differential IEC response via selective activation of TLR5. These functional differences are dependent on specific motifs in non-conserved regions of their D0 domains. Supported by R01 AI162736, R21 DK118386, T32 AI007051.

The extracellular tail of IFITM3 promotes SARS-CoV-2 entry into cells and is diversifying in primates

Abstract The interferon-induced transmembrane (IFITM) proteins confer cells with resistance to diverse virus infections by altering membrane biomechanics and disfavoring virus-cell membrane fusion. Human IFITM3 strongly restricts SARS-CoV and MERS Spike-mediated infections in endosomes. However, work from our labs demonstrated that IFITM3 has opposing effects on SARS-CoV-2 (SCV2) infection: IFITM3 in endosomes restricts SCV2 infection, but IFITM3 at the cell surface enhances SCV2 infection. In the present study, we investigated the determinants governing the enhancement of SCV2 infection by human IFITM3. Using clinical isolates of SCV2 and pseudoviruses bearing SCV2 Spike, we found that the penultimate and ultimate amino acid residues of IFITM3, which are predicted to extend into the extracellular space, are essential for enhancement of SCV2 Spike-mediated infection. Deletion of these residues in human IFITM3 resulted in loss of SCV2 infection enhancement. On the other hand, we found that certain non-human IFITM3 proteins enhanced SCV2 infection to a greater extent than human IFITM3, and this mapped to sequence divergence in the penultimate and ultimate residues of the IFITM3 extracellular tail. Transferring the last two amino acids of macaque IFITM3 to human IFITM3 resulted in further enhancement of SCV2 infection. These results indicate that certain non-human primate IFITM3 proteins may be poised to act as potent enhancers of SCV2 infection in those species. Genomic analyses revealed that the IFITM3 extracellular tail is diversifying rapidly and recurrently in primates over evolutionary time, raising the possibility that variation at these sites is adaptive in nature and allows for escape from co-option by coronaviruses. NIH Intramural Research Program NIAID Intramural Targeted Anti-COVID19 Program Award

Two new species of green treefrogs (Pelodryadidae: Litoria) from the northern slopes of Papua New Guinea's Central Cordillera.

We describe two new species of moderate-sized (male body length 26.5-29.8 mm and 41.0 mm), predominantly green treefrogs in the genus Litoria from hill forest on the northern slopes of Papua New Guinea's Central Cordillera. Phylogenetic analysis of mitochondrial ND4 nucleotide sequences shows that the first species is related to Litoria iris (Tyler) and its allies. It is morphologically most similar to Litoria mystax, a small green treefrog known only from the holotype that was described more than 100 years ago from the north coast of western New Guinea but differs from that species in having longer legs and a broader head. The second species is closest to Litoria gasconi, a species known only from the foothills of the Foja Mountains in Papua Province, Indonesian New Guinea, and the Prince Alexander Mountains in northern Papua New Guinea. It has a net average sequence divergence of 10% from L. gasconi and can be distinguished morphologically from it and from other pelodryadids by the presence of a striking pattern of spots and blotches on the ventral surfaces and on the hidden surfaces of the limbs. These descriptions add to the rapidly increasing known diversity of frogs in hill and lower montane forest, habitats that support the most diverse frog communities on mainland New Guinea.

HLA-DP diversity is associated with improved response to SARS-Cov-2 vaccine in hematopoietic stem cell transplant recipients

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients show lower humoral vaccine responsiveness than immunocompetent individuals. HLA diversity, measured by the HLA evolutionary divergence (HED) metrics, reflects the diversity of the antigenic repertoire presented to Tcells, and has been shown to predict response to cancer immunotherapy. We retrospectively investigated the association of HED with humoral response to SARS-CoV-2 vaccine in allo-HSCT recipients. HED was calculated as pairwise genetic distance between alleles at HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 loci in recipients and their donors. Low anti-spike IgG levels (<30 BAU/mL) were associated with short time from allo-SCT and low donor DPB1-HED, mostly related to donor DPB1 homozygosity. The diversity of donor HLA-DP molecules, assessed by heterozygosity or sequence divergence, may thus impact the efficacy of donor-derived CD4 Tcells to sustain vaccine-mediated antibody response in allo-HSCT recipients.

Mapping the Chemical Space of Active-Site Targeted Covalent Ligands for Protein Tyrosine Phosphatases.

Protein tyrosine phosphatases (PTPs) are an important class of enzymes that modulate essential cellular processes through protein dephosphorylation and are dysregulated in various disease states. There is demand for new compounds that target the active sites of these enzymes, for use as chemical tools to dissect their biological roles or as leads for the development of new therapeutics. In this study, we explore an array of electrophiles and fragment scaffolds to investigate the required chemical parameters for covalent inhibition of tyrosine phosphatases. Our analysis juxtaposes the intrinsic electrophilicity of these compounds with their potency against several classical PTPs, revealing chemotypes that inhibit tyrosine phosphatases while minimizing excessive, potentially non-specific reactivity. We also assess sequence divergence at key residues in PTPs to explain their differential susceptibility to covalent inhibition. We anticipate that our study will inspire new strategies to develop covalent probes and inhibitors for tyrosine phosphatases.

Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance.

Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.

On the Ideal Convergent Sequences in Fuzzy Normed Space

This article discusses a variety of important notions, including ideal convergence and ideal Cauchyness of topological sequences produced by fuzzy normed spaces. Furthermore, the connections between the concepts of the ideal limit and ideal cluster points of a sequence in a fuzzy normed linear space are investigated. In a fuzzy normed space, we investigated additional effects, such as describing compactness in terms of ideal cluster points and other relevant but previously unresearched ideal convergence and adjoint ideal convergence aspects of sequences and nets. The countable compactness of a fuzzy normed space and its link to it were also defined. The terms ideal and its adjoint divergent sequences are then introduced, and specific aspects of them are explored in a fuzzy normed space. Our study supports the importance of condition (AP) in examining summability via ideals. It is suggested to use a fuzzy point symmetry-based genetic clustering method to automatically count the number of clusters in a data set and determine how well the data are fuzzy partitioned. As long as the clusters have the attribute of symmetry, they can be any size, form, or convexity. One of the crucial ways that symmetry is used in fuzzy systems is in the solution of the linear Fuzzy Fredholm Integral Equation (FFIE), which has symmetric triangular (Fuzzy Interval) output and any fuzzy function input.

Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi.

Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species' breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics.

Promoter evolution of mammalian gene duplicates

BackgroundGene duplication is thought to be a central process in evolution to gain new functions. The factors that dictate gene retention following duplication as well paralog gene divergence in sequence, expression and function have been extensively studied. However, relatively little is known about the evolution of promoter regions of gene duplicates and how they influence gene duplicate divergence. Here, we focus on promoters of paralog genes, comparing their similarity in sequence, in the sets of transcription factors (TFs) that bind them, and in their overall promoter architecture.ResultsWe observe that promoters of recent duplications display higher sequence similarity between them and that sequence similarity rapidly declines between promoters of more ancient paralogs. In contrast, similarity in cis-regulation, as measured by the set of TFs that bind promoters of both paralogs, does not simply decrease with time from duplication and is instead related to promoter architecture—paralogs with CpG Islands (CGIs) in their promoters share a greater fraction of TFs, while CGI-less paralogs are more divergent in their TF binding set.Focusing on recent duplication events and partitioning them by their duplication mechanism enables us to uncover promoter properties associated with gene retention, as well as to characterize the evolution of promoters of newly born genes: In recent retrotransposition-mediated duplications, we observe asymmetry in cis-regulation of paralog pairs: Retrocopy genes are lowly expressed and their promoters are bound by fewer TFs and are depleted of CGIs, in comparison with the original gene copy. Furthermore, looking at recent segmental duplication regions in primates enable us to compare successful retentions versus loss of duplicates, showing that duplicate retention is associated with fewer TFs and with CGI-less promoter architecture.ConclusionsIn this work, we profiled promoters of gene duplicates and their inter-paralog divergence. We also studied how their characteristics are associated with duplication time and duplication mechanism, as well as with the fate of these duplicates. These results underline the importance of cis-regulatory mechanisms in shaping the evolution of new genes and their fate following duplication.