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Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis.

Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7Gb of sequence data, with raw reads ranging from 1.2Gb for Caspian horses to 0.38Gb for Turkoman horses. Post-filtering, approximately 1.9Gb of reads remained, with ~ 1.5Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.

Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods

BackgroundCamellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera’s ability to adapt to different photoperiods.ResultsOur results indicate that the photoperiod can significantly impact flowering time in C. oleifera. We grew a total of nine samples under the short day condition (SD), middle day condition (MD) and long day condition (LD). Transcriptome analysis yielded 66.94 Gb of high-quality clean reads, with an average of over 6.73 Gb of reads for per sample. Following assembly, a total of 120,080 transcripts were obtained and 94,979 unigenes annotated. A total of 3475 differentially expressed genes (DEGs) were identified between the SD_MD, SD_LD, and MD_LD gene sets. Moreover, WGCNA identified ten gene modules. Genes in pink module (92 genes) were positively correlated with SD, and negatively correlated with both MD and LD. Genes in the magenta module (42 genes) were positively correlated with MD and negatively correlated with both LD and SD. Finally, genes in the yellow module (1758 genes) were positively correlated with both SD and MD, but negatively correlated with LD. KEGG enrichment analysis revealed that genes in the pink, magenta, and yellow modules were involved in flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism and circadian rhythm pathways. Additionally, eight hub genes (GI, AP2, WRKY65, SCR, SHR, PHR1, ERF106, and SCL3) were obtained through network analysis. The hub genes had high connectivity with other photoperiod-sensitive DEGs. The expression levels of hub genes were verified by qRT-PCR analysis.ConclusionAn increase in light duration promotes earlier flowering of C. oleifera. Flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, and circadian rhythm pathways may function in the photoperiodic flowering pathway of C. oleifera. We also identified eight hub genes that may play a role in this pathway. Ultimately, this work contributes to our understanding of the photoperiodic flowering pathway of C. oleifera and further informs molecular breeding programs on the plant’s photoperiodic sensitivity.

Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge

BackgroundThere is concern that the microbially rich activated sludge environment of wastewater treatment plants (WWTPs) may contribute to the dissemination of antibiotic resistance genes (ARGs). We applied long-read (nanopore) sequencing to profile ARGs and their neighboring genes to illuminate their fate in the activated sludge treatment by comparing their abundance, genetic locations, mobility potential, and bacterial hosts within activated sludge relative to those in influent sewage across five WWTPs from three continents.ResultsThe abundances (gene copies per Gb of reads, aka gc/Gb) of all ARGs and those carried by putative pathogens decreased 75–90% from influent sewage (192-605 gc/Gb) to activated sludge (31-62 gc/Gb) at all five WWTPs. Long reads enabled quantification of the percent abundance of ARGs with mobility potential (i.e., located on plasmids or co-located with other mobile genetic elements (MGEs)). The abundance of plasmid-associated ARGs decreased at four of five WWTPs (from 40–73 to 31–68%), and ARGs co-located with transposable, integrative, and conjugative element hallmark genes showed similar trends. Most ARG-associated elements decreased 0.35–13.52% while integrative and transposable elements displayed slight increases at two WWTPs (1.4–2.4%). While resistome and taxonomic compositions both shifted significantly, host phyla for chromosomal ARG classes remained relatively consistent, indicating vertical gene transfer via active biomass growth in activated sludge as the key pathway of chromosomal ARG dissemination.ConclusionsOverall, our results suggest that the activated sludge process acted as a barrier against the proliferation of most ARGs, while those that persisted or increased warrant further attention.CRgUGB86FqkKDWfHB8LKXnVideo abstract

Mining cytochrome p450 genes through next generation sequencing and metagenomic analysis from Binh Chau hot spring

Cytochrome P450s (CYPs) are one of the largest distributed enzymes, which catalyze more than 20 different reactions. At present, there has been an increasing realization of the power of P450 biocatalysts for the industrial synthesis of pharmaceuticals, agrochemicals, bulk chemicals, food ingredients, etc. On the other hand, the conditions of industrial processes at high temperature, high-pressure or in chemical solvent require the enzymes, which catalyze the bioconversion, have a specific properties such as thermostability, chemical tolerance or barophilicity. Up to date, the number of thermostable P450s is limited. Nowadays, DNA-metagenome technique gives us a chance to catch novel genes and unique interesting enzymes from microbial community in certain ecology. In this paper, metagenomic DNA extracted from water samples from Binh Chau hot spring was sequenced using Illumila’s HiSeq platform and was analysed to mining putative genes encoding cytochrome P450. The sequencing generated 9.4 Gb of reads containing 156,093 putative ORFs, of these, 106,903 genes were annotated in NCBI non-redundant protein sequence database. Among all the ORFs were annotated, 68 putative ORFs encoding cytochrome P450 were found belong to 36 specific groups of cytochrome P450 protein family. Of these, the melting temperature (Tm) from thirty-six completed ORFs was predicted for a better understanding of thermodynamic stability.

Mining cytochrome p450 genes through next generation sequencing and metagenomic analysis from Binh Chau hot spring

Cytochrome P450s (CYPs) are one of the largest distributed enzymes, which catalyze more than 20 different reactions. At present, there has been an increasing realization of the power of P450 biocatalysts for the industrial synthesis of pharmaceuticals, agrochemicals, bulk chemicals, food ingredients, etc. On the other hand, the conditions of industrial processes at high temperature, high-pressure or in chemical solvent require the enzymes, which catalyze the bioconversion, have a specific properties such as thermostability, chemical tolerance or barophilicity. Up to date, the number of thermostable P450s is limited. Nowadays, DNA-metagenome technique gives us a chance to catch novel genes and unique interesting enzymes from microbial community in certain ecology. In this paper, metagenomic DNA extracted from water samples from Binh Chau hot spring was sequenced using Illumila’s HiSeq platform and was analysed to mining putative genes encoding cytochrome P450. The sequencing generated 9.4 Gb of reads containing 156,093 putative ORFs, of these, 106,903 genes were annotated in NCBI non-redundant protein sequence database. Among all the ORFs were annotated, 68 putative ORFs encoding cytochrome P450 were found belong to 36 specific groups of cytochrome P450 protein family. Of these, the melting temperature (Tm) from thirty-six completed ORFs was predicted for a better understanding of thermodynamic stability.

Whole-Transcriptome Analysis of Differentially Expressed Genes in the Vegetative Buds, Floral Buds and Buds of Chrysanthemum morifolium

Background Chrysanthemum morifolium is an important floral crop that is cultivated worldwide. However, due to a lack of genomic resources, very little information is available concerning the molecular mechanisms of flower development in chrysanthemum.ResultsThe transcriptomes of chrysanthemum vegetative buds, floral buds and buds were sequenced using Illumina paired-end sequencing technology. A total of 15.4 Gb of reads were assembled into 91,367 unigenes with an average length of 739 bp. A total of 43,137 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 25,424, 24,321 and 13,704 unigenes were assigned to 56 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1,876 differentially expressed genes (DEGs) (1,516 up-regulated, 360 down-regulated) were identified between vegetative buds and floral buds, and 3,300 DEGs (1,277 up-regulated, 1,706 down-regulated) were identified between floral buds and buds. Many genes encoding important transcription factors (e.g., AP2, MYB, MYC, WRKY, NAC and CRT) as well as proteins involved in carbohydrate metabolism, protein kinase activity, plant hormone signal transduction, and the defense responses, among others, were considerably up-regulated in floral buds. Genes involved in the photoperiod pathway and flower organ determination were also identified. These genes represent important candidate genes for molecular cloning and functional analysis to study flowering regulation in chrysanthemum.ConclusionThis comparative transcriptome analysis revealed significant differences in gene expression and signaling pathway components between the vegetative buds, floral buds and buds of Chrysanthemum morifolium. A wide range of genes was implicated in regulating the phase transition from vegetative to reproductive growth. These results should aid researchers in the study of flower-time regulation, breeding and molecular biology in chrysanthemum.