Coding DNA Sequences Research Articles

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes.

OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes. We collect gene annotations, delineate hierarchical gene orthologyand annotate the orthologous groups (OGs) with functional and evolutionary traits. OrthoDB is the leading resource for species diversity, striving to sample the most diverse and well-researched organisms with the highest quality genomic data. This update expands to include 5827 eukaryotic genomes. We have also added coding DNA sequences (CDSs) and gene loci coordinates. OrthoDB can be browsed, downloaded, or accessed using REST API, SPARQL/RDFand now also via API packages for Python and R Bioconductor. OrthoLoger (https://orthologer.ezlab.org), the tool used for inferring orthologs in OrthoDB, is now available as a Conda package and through BioContainers. ODB-mapper, a component of OrthoLoger, streamlines annotation of genes from newly sequenced genomes with OrthoDB evolutionary and functional descriptors. The benchmarking sets of universal single-copy orthologs (BUSCO), derived from OrthoDB, had correspondingly a major update. The BUSCO tool (https://busco.ezlab.org) has become a standard in genomics, uniquely capable of assessing both eukaryotic and prokaryotic species. It is applicable to gene sets, transcriptomes, genome assembliesand metagenomic bins.

Comparison of the Distribution Patterns of Microsatellites Across the Genomes of Reptiles

ABSTRACTMicrosatellites or simple sequence repeats (SSRs) are prevalent across various organisms' genomes. However, their distribution patterns and evolutionary dynamics in reptile genomes are rarely studied systematically. We herein conducted a comprehensive analysis of SSRs in the genomes of 36 reptile species. Our findings revealed that the total number of SSRs ranged from 1,840,965 to 7,664,452, accounting for 2.16%–8.19% of the genomes analyzed. The relative density ranged from 21,567.82 to 81,889.41 bp per megabase (Mbp). The abundance of different SSR categories followed the pattern of imperfect SSR (I‐SSR) > perfect SSR (P‐SSR) > compound SSR (C‐SSR). A significant positive correlation was observed between the number of SSRs and genome size (p = 0.0034), whereas SSR frequency (p = 0.013) or density (p = 0.0099) showed a negative correlation with genome size. Furthermore, no correlation was found between SSR length and genome size. Mononucleotide repeats were the most common P‐SSRs in crocodilians and turtles, whereas mononucleotides, trinucleotides, or tetranucleotides were the most common P‐SSRs in snakes, lizards, and tuatara. P‐SSRs of varying motif sizes showed nonrandom distribution across different genic regions, with AT‐rich repeats being predominant. The genomic SSR content of the squamate lineage ranked the highest in abundance and variability, whereas crocodilians and turtles showed a slowly evolving and reduced microsatellite landscape. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that genes harboring P‐SSRs in the coding DNA sequence regions were primarily involved in the regulation of transcription and translation processes. The SSR dataset generated in this study provides potential candidates for functional analysis and calls for broader‐scale analyses across the evolutionary spectrum.

Mapping the locus for ocular melanosis in Cairn Terriers.

To map the disease locus for familial ocular melanosis (OM) in the Cairn Terrier. Cairn Terriers with OM and normal control dogs. A genome-wide association study (GWAS) was performed using 63 OM-affected and 31 control Cairn Terriers, followed by haplotype analysis. A significantly associated single-nucleotide polymorphism was genotyped in a larger group of OM-affected and control Cairn Terriers. The coding and splice-site regions of genes mapping within the confidence interval were sequenced. A ~9.2 Mb region of chromosome 11 was significantly associated with OM. Haplotype analysis narrowed the region to 1.49 Mb. Genotyping of a SNP within the region showed 86% of OM-affected dogs were homozygous or heterozygous for the risk allele, whereas 78% of unaffected dogs were homozygous for the nonrisk allele. Sequencing of the coding regions and splice sites of four genes (c9orf72, IFNK, the 5' end of MOB3B, and the 3' end of LINGO2) and of a microRNA (MIR876) did not detect any genetic variants unique to OM-affected dogs. OM in Cairn Terriers maps to a 1.49 Mb region of chromosome 11. This accounts for 86% of OM cases in our DNA bank. A second locus may account for the OM phenotype in the remaining 14% of cases. Sequencing of coding regions and splice sites of positional candidate genes and a microRNA did not reveal any genetic variants unique to affected dogs. Further studies are required to elucidate the DNA variant causal for OM in Cairn Terriers and to understand the disease mechanism.

Exploring the longitudinal expression dynamics of midguts in adult female Amblyomma americanum ticks

BackgroundFemale ticks remain attached to their host for multiple days to complete a blood meal. This prolonged feeding period is accompanied by a significant increase in the tick’s size and body weight, paralleled by noteworthy changes to the tick midgut. While the midgut is recognized for its established role in blood storage and processing, its importance extends to playing a crucial role in the acquisition, survival, and proliferation of pathogens. Despite this, our overall understanding of tick midgut biology is limited.ResultsOur transcriptome analysis identified 15,599 putative DNA coding sequences (CDS), which were classified into 26 functional groups. Dimensional and differential expression analyses revealed four primary transcriptional profiles corresponding to unfed, slow-feeding, transitory (from slow- to rapid-feeding), and rapid-feeding stages. Additionally, comparing the current dataset with previously deposited transcriptome from other tick species allowed the identification of commonly expressed transcripts across different feeding stages.ConclusionOur findings provide a detailed temporal resolution of numerous metabolic pathways in the midgut of A. americanum adult females throughout the feeding process, highlighting the dynamic transcriptional regulation of the tick’s midgut as feeding progresses. Furthermore, we identified conserved transcripts across three different tick species that exhibit similar expression patterns. This knowledge not only enhances our understanding of the physiological processes within the tick midgut but also opens up potential avenues for developing control methods that target multiple tick species.

Probiotic and fermentation properties of Leuconostoc mesenteroides strain I1/53 from sugarcane juice by a multi-omics approach

Previous studies have demonstrated the presence of microorganisms in sugarcane juice, but the species composition and characteristics of dominant strains remain ambiguous. In this study, the most abundant strain Leuconostoc mesenteroides accounted for 39.89% of the total sequences in sugarcane juice. Subsequently, a L. mesenteroides, here named as strain I1/53, was isolated on a typical MRS medium. The whole genome size of the isolate was 2,044,872 bp with a GC content of 37.5% and 2027 coding DNA sequences with average length of 907 bp. Notably, the strain involved no antibiotic-related and virulence factor-producing genes, not producing endotoxins. In contrast, the L. mesenteroides I1/53 contained abundant adaptability and stress tolerance response genes of the human gastrointestinal environment. Additionally, strain I1/53 potentially encoded bacteriocin lactococcin G by expressing lagD, and demonstrated its antibacterial efficacy against Gram-positive and negative foodborne pathogens by in-vitro experiments. The fermentation of the strain I1/53 significantly elevated beneficial metabolites such as SCFAs, liquiritigenin, L-catechin, α-solanine and indoleacetic acid, whereas deleted harmful compounds for human wellness, including valdecoxib. Therefore, this study demonstrates the probiotic and fermentation properties of the dominant L. mesenteroides in sugarcane juice, which provide a robust theoretical foundation for its application in foods as a probiotic.

Characterisation of C-C Ligand 7 (CCL7) as Asthma Genetic Marker in Pigtailed Monkey.

The pigtailed monkey (Macaca nemestrina) is one of the species that have potency like the cynomolgus monkey that is widely used as an animal model for asthma study. The CCL7 gene has potential as a genetic marker because of the secreted chemokine that plays a role in asthma. The aims of this research are to characterise the CCL7 gene of pigtailed monkey, compare the structure of their CCL7 gene with other primate species and determine model 3D structure protein prediction of CCL7 protein. The amplicons were sequenced, and the results were analysed by the bioinformatics technique. The 3D CCL7 protein structure was predicted using I-TASSER. We have isolated 2221 bp sequences CCL7 gene and 109 amino acids from pigtailed monkey. Variation of CCL7 gene sequence between pigtailed monkey and other primate species (Macaca fascicularis, M. mulatta and Homo sapiens) was found in exon 1, exon 2 and exon 3 as CDS (Coding DNA Sequence) region. The analysis homology of nucleotides and amino acid sequences of the CCL7 gene indicated that the pigtailed monkey and three other primate species have a high homology rate with an identity score above 90%. Meanwhile, a comparative analysis of CDS and amino acid regions showed that the pigtailed monkey also has the highest similarity with the three other primate species with more than 90% identity score. The 3D structure protein prediction model of the CCL7 pigtailed monkey revealed the highest similarity with H. sapiens with an identity value of about 95%. Therefore, the pigtailed monkey CCL7 gene has high similarity with H. sapiens, which means that based on molecular similarity, the pigtailed monkey has the potential to be an animal model for asthma study, especially the study of molecular and the role of CCL7 in asthma pathogenesis.

Draft genome sequence of Listeria aquatica strain SG_BD1, isolated from a cow dung sample in Bangladesh.

Here, we present the genome of Listeria aquatica strain SG_BD1, isolated from cow dung in Dhaka, Bangladesh, and assembled after Oxford Nanopore sequencing. The genome is 2,690,148 bp with 2,855 predicted coding DNA sequences, G + C content of 39.6%, and displays a putative virulence gene clpP and 9 CRISPRs.

Exploring midgut expression dynamics: longitudinal transcriptomic analysis of adult female Amblyomma americanum midgut and comparative insights with other hard tick species.

Female ticks remain attached to their host for multiple days to complete a blood meal. This prolonged feeding period is accompanied by a significant increase in the tick's size and body weight, paralleled by noteworthy changes to the tick midgut. While the midgut is recognized for its established role in blood storage and processing, its importance extends to playing a crucial role in the acquisition, survival, and proliferation of pathogens. Despite this, our overall understanding of tick midgut biology is limited. We conducted a comprehensive longitudinal transcriptome analysis of the midgut in adult female A. americanum ticks across various feeding stages, including unfed, slow-feeding, and rapid-feeding phases. Our analysis revealed 15,599 putative DNA coding sequences (CDS) classified within 26 functional groups. Dimensional and differential expression analysis highlighted the dynamic transcriptional changes in the tick midgut as feeding progresses, particularly during the initial period of feeding and the transition from the slow-feeding to the rapid-feeding phase. Additionally, we performed an orthology analysis comparing our dataset with midgut transcriptomes from other hard ticks, such as Ixodes scapularis and Rhipicephalus microplus. This comparison allowed us to identify transcripts commonly expressed during different feeding phases across these three species. Our findings provide a detailed temporal resolution of numerous metabolic pathways in A. americanum, emphasizing the dynamic transcriptional changes occurring in the tick midgut throughout the feeding process. Furthermore, we identified conserved transcripts across three different tick species that exhibit similar expression patterns. This knowledge has significant implications for future research aimed at deciphering the physiological pathways relevant within the tick midgut. It also offers potential avenues for developing control methods that target multiple tick species.

Comparison of Mycobacterium tuberculosis Strains with H37Rv Using Whole Genome Sequence Analysis to Identify Virulence Factors and Phylogenetic Relationships

Mycobacterium tuberculosis (Mtb) poses a significant disease burden in developing countries, largely due to the rising issue of drug resistance. In Pakistan, the genetic and molecular characteristics of resistant strains have not been thoroughly analyzed or compared with the reference Mtb strain, H37Rv, to understand the molecular and genetic epidemiology. Mtb employs various strategies to resist anti-tuberculosis drugs, and antimicrobial resistance, including single and multidrug resistance, has increased extensively in developing nations like Pakistan. In this study, the whole genomes of three Mtb strains (335, 335-2, and 311) were uploaded to the Rapid Annotation Subsystems Technology (RAST) server to retrieve coding DNA sequences (CDS). The RAST server identified 4,454, 4,445, and 4,396 CDS for Mtb strains 335, 335-2, and 311, respectively. Mutation analysis was performed using NCBI nucleotide BLAST and CLUSTAL Omega, comparing the sequences with the H37Rv reference strain. The analysis revealed 909, 832, and 1,135 mutations in the 335, 335-2, and 311 strains, respectively. Phylogenetic analysis based on the most virulent protein (EccC3) indicated a close resemblance between all three strains and the H37Rv strain. Furthermore, Mycobacteriumcanettii (accession number WP_203037448.1) was identified as the closest related bacterium to the studied strains and H37Rv.

Are genomic language models all you need? Exploring genomic language models on protein downstream tasks.

Large language models, trained on enormous corpora of biological sequences, are state-of-the-art for downstream genomic and proteomic tasks. Since the genome contains the information to encode all proteins, genomic language models (gLMs) hold the potential to make downstream predictions not only about DNA sequences, but also about proteins. However, the performance of gLMs on protein tasks remains unknown, due to few tasks pairing proteins with the coding DNA sequences (CDS) that can be processed by gLMs. In this work, we curated five such datasets and used them to evaluate the performance of gLMs and proteomic language models (pLMs). We show that gLMs are competitive and even outperform their pLMs counterparts on some tasks. The best performance was achieved using the retrieved CDS compared to sampling strategies. We found that training a joint genomic-proteomic model outperforms each individual approach, showing that they capture different but complementary sequence representations, as we demonstrate through model interpretation of their embeddings. Lastly, we explored different genomic tokenization schemes to improve downstream protein performance. We trained a new Nucleotide Transformer (50M) foundation model with 3mer tokenization that outperforms its 6mer counterpart on protein tasks while maintaining performance on genomics tasks. The application of gLMs to proteomics offers the potential to leverage rich CDS data, and in the spirit of the central dogma, the possibility of a unified and synergistic approach to genomics and proteomics. We make our inference code, 3mer pre-trained model weights and datasets available.

Potent pollen gene regulation by DNA glycosylases in maize.

Although DNA methylation primarily represses TEs, it also represses select genes that are methylated in plant body tissues but demethylated by DNA glycosylases (DNGs) in endosperm or pollen. Activity of either one of two DNGs, MDR1 or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen segregating mutations in both genes, we identified 58 candidate DNG target genes that account for 11.1% of the wild-type transcriptome but are silent or barely detectable in the plant body (sporophyte). They are unusual in their tendency to lack introns but even more so in their having TE-like methylation in their CDS. The majority have predicted functions in cell wall modification, and they likely support the rapid tip growth characteristic of pollen tubes. These results suggest a critical role for DNA methylation and demethylation in regulating maize genes with potential for extremely high expression in pollen but constitutive silencing elsewhere.

Assembly and Annotation of the Complete Genome Sequence of the Paenibacillus Bacteriophage phJNUCC32

A potential biocontrol agent for American foulbrood (AFB), the Paenibacillus bacteriophage phJNUCC32, was isolated from Baengnokdam in Halla Mountain. This study aimed to investigate its genomic characteristics through whole-genome sequencing. The genome of phJNUCC32 was found to be 62,871 base pairs in length, with a G + C content of 51.98%. Phylogenetic analysis classified phJNUCC32 within the unclassified Caudoviricetes bacteriophage category. The genome prediction confirmed the absence of virulence factors and antibiotic-resistance genes, ensuring its genetic safety. A total of 63 coding DNA sequences were identified, revealing a modular arrangement. Notably, the annotation of gene function indicates that phJNUCC32 harbors the holin/lysin system, suggesting significant potential for controlling bacterial infections in AFB and agriculture.

An Updated Canvas of the RFC1-mediated CANVAS (Cerebellar Ataxia, Neuropathy and Vestibular Areflexia Syndrome).

Proliferation of specific nucleotide sequences within the coding and non-coding regions of numerous genes has been implicated in approximately 40 neurodegenerative disorders. Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), a neurodegenerative disorder, is distinguished by a pathological triad of sensory neuropathy, bilateral vestibular areflexia and cerebellar impairments. It manifests in adults gradually and is autosomal recessive and multi-system ataxia. Predominantly, CANVAS is associated with biallelic AAGGG repeat expansions in intron 2 of the RFC1 gene. Although various motifs have been identified, only a subset induces pathological consequences, by forming stable secondary structures that disrupt gene functions both in vitro and in vivo. The pathogenesis of CANVAS remains a subject of intensive research, yet its precise mechanisms remain elusive. Herein, we aim to comprehensively review the epidemiology, clinical ramifications, molecular mechanisms, genetics, and potential therapeutics in light of the current findings, extending an overview of the most significant research on CANVAS.

Draft genome of a biological control agent against Bipolaris sorokiniana, the causal phytopathogen of spot blotch in wheat (Triticum turgidum L. subsp. durum): Bacillus inaquosorum TSO22

Abstract Strain TSO22 was isolated from bulk soil associated with wheat crops in the Yaqui Valley, Mexico. The draft genome contained 4,294,671 bp, 43.7% G + C content, 731,759 bp N50, 3 L50, and 29 contigs. Based on 16S rRNA gene sequencing, the overall genome relatedness index, and phylogenomic relationship, strain TSO22 is highly affiliated with Bacillus inaquosorum. Genome annotation revealed 94 RNAs and 4,465 predicted coding DNA sequences distributed in 336 subsystems, in which genes involved in plant growth promotion and biocontrol were detected, such as colonizing plant system, competitive exclusionist, control of biotic and abiotic stresses, and plant immune response stimulation. Genomic predictions were confirmed through in vitro analysis, which revealed that B. inaquosorum TSO22 has great biological control against Bipolaris sorokiniana, as well as excellent metabolic capabilities to improve plant growth and development.

Draft genome of the marine bacterium Alteromonas gracilis strain J4 isolated from the green coenocytic alga Caulerpa prolifera.

Here, we present the draft genome sequence of Alteromonas gracilis strain J4, isolated from the green macroalga Caulerpa prolifera. The draft genome is 4,492,914 bp in size and contains 4,719 coding DNA sequences, 67 tRNAs, and 16 rRNA-coding genes. Strain J4 may exhibit host growth-promoting properties.

The systematic codon usage bias has an important effect on genetic adaption in native species

Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.

Genome Analysis of Pseudomonas viciae G166 Conferring Antifungal Activity in Grapevine.

Grapevine (Vitis vinifera) is one of the major economic fruit crops but suffers many diseases, causing damage to the quality of grapes. Strain G166 was isolated from the rhizosphere of grapevine and was found to exhibited broad-spectrum antagonistic activities against fungal pathogens on grapes in vitro, such as Coniella diplodiella, Botrytis cinerea, and Colletotrichum gloeosporioides. Whole-genome sequencing revealed that G166 contained a 6,613,582 bp circular chromosome with 5749 predicted coding DNA sequences and an average GC content of 60.57%. TYGS analysis revealed that G166 belongs to Pseudomonas viciae. Phenotype analysis indicated that P. viciae G166 remarkably reduced the severity of grape white rot disease in the grapevine. After inoculation with C. diplodiella, more H2O2 and MDA accumulated in the leaves and resulted in decreases in the Pn and chlorophyll content. Conversely, G166-treated grapevine displayed less oxidative damage with lower H2O2 levels and MDA contents under the pathogen treatments. Subsequently, G166-treated grapevine could sustain a normal Pn and chlorophyll content. Moreover, the application of P. viciae G166 inhibited the growth of mycelia on detached leaves and berries, while more disease symptoms occurred in non-bacterized leaves and berries. Therefore, P. viciae G166 served as a powerful bioagent against grape white rot disease. Using antiSMASH prediction and genome comparisons, a relationship between non-ribosomal peptide synthase clusters and antifungal activity was found in the genome of P. viciae G166. Taken together, P. viciae G166 shows promising antifungal potential to improve fruit quality and yield in ecological agriculture.

Knockdown of NFIC Promotes Bovine Myoblast Proliferation through the CENPF/CDK1 Axis.

As cellular transcription factors and DNA replicators, nuclear factor I (NFI) family members play an important role in mammalian development. However, there is still a lack of research on the muscle regeneration of NFI family members in cattle. In this study, the analysis of NFI family factors was conducted on their characterization, phylogenetics, and functional domains. We found that NFI family members were relatively conserved among different species, but there was heterogeneity in amino acid sequences, DNA coding sequences, and functional domain among members. Furthermore, among NFI family factors, we observed that NFIC exhibited highly expression in bovine muscle tissues, particularly influencing the expression of proliferation marker genes in myoblasts. To investigate the influence of NFIC on myoblast proliferation, we knocked down NFIC (si-NFIC) and found that the proliferation of myoblasts was significantly promoted. In terms of regulation mechanism, we identified that si-NFIC could counteract the inhibitory effect of the cell cycle inhibitor RO-3306. Interestingly, CENPF, as the downstream target gene of NFIC, could affect the expression of CDK1, CCNB1, and actively regulate the cell cycle pathway and cell proliferation. In addition, when CENPF was knocked down, the phosphorylation of p53 and the expression of Bax were increased, but the expression of Bcl2 was inhibited. Our findings mainly highlight the mechanism by which NFIC acts on the CENPF/CDK1 axis to regulate the proliferation of bovine myoblasts.

Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

In silico modelling of proteins encoded by important genes of flavonoid biosynthesis pathway in Gymnema sylvestre R. Br.

Understanding the proteins and metabolites produced by plants aids in developing superior planting materials. Gymnema sylvestre, a significant medicinal plant containing beneficial compounds such as oleanane, dammarane, flavonoids and gymnemic acids, exhibiting antioxidant and antidiabetic properties, making it a promising alternative treatment for Type 2 diabetes with minimal side effects. Transcriptomics in G. sylvestre yielded Coding DNA Sequences (CDS) for 12 key genes of flavonoid biosynthesis. Translated protein sequences of those 12 genes underwent characterization using protPARAM and i-TASSER. In silico protein modelling found similarities to validated enzymes, suggesting functional potential of the studied proteins. The study enlightens the first comprehensive insight into key proteins involved in G. sylvestre's flavonoid biosynthesis pathway. GsCHS (G. sylvestre chalcone synthase), a key enzyme in flavonoid biosynthesis, corroborated its phylogenetic proximity to Vincetoxicum mongolicum's CHS. Protein docking analysis delineated the distinctive features of GsCHS from cpCHS1 of Cyclosorus parasiticus, particularly in its substrate binding pockets and interactive sites crucial for synthesizing essential flavonoids.