DNA Research最新文献

Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of two wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. A syntenic analysis of the G. hybrida genome and published Asterales genomes demonstrated that Gerbera has undergone a whole-genome triplication. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

The diatom Pleurosigma pacificum is a newly described tropical pelagic species from the Western Pacific Ocean with one of largest genome size among published diatom genomes, making it an ideal candidate for studying adaptation to tropical open ocean environments and diatom evolution. We employed HiFi long-read sequencing to construct a high-quality and contaminant-free genome. The assembled genome is 1.357 Gb in size and consists of 821 contigs with a contig N50 of 3.23 Mb. The GC content is 38.6%, which is much lower than that of other published diatom genomes. The genome contains 27,408 predicted genes, 540 of which were implicated in environmental adaptation. Gene features and gene family comparisons suggest that the primary driver of genome expansion and functional diversification is long terminal repeats (LTR) retrotransposons and tandem duplications. The phylogenetic analysis revealed that the clade of P. pacificum is closely associated with other members of Naviculales. The expansion of chlorophyll a/c proteins might facilitate the adaptation of P. pacificum to high-light conditions in pelagic environments. The percentage of approximately 3.2% horizontal gene transfer (HGT) events is observed in the P. pacificum genome. HGTs are a prevalent phenomenon in diatoms and serve as a common mechanism to enhance their adaptive capabilities. In conclusion, the P. pacificum genome provides important understanding into the development of large genome size and evolutionary adaptations of pelagic diatoms.

Nontuberculous mycobacteria occasionally harbour clustered tRNA genes, referred to as a tRNA array unit, which is considered a putative antidefense system within their genomes. However, the precise genomic location of these tRNA array units remains unclear. To address this, we sequenced the complete genomes of 5 Mycobacterium avium strains carrying a tRNA array unit using a hybrid assembly of long and short reads followed by manual curation. The assemblies indicated that each strain harbours 3 to 5 extrachromosomal elements. In all genomes, the tRNA array unit was found on a linear contig exceeding 300 kb. Pulse-field gel electrophoresis (PFGE) and sodium dodecyl sulphate-PFGE revealed that the strains harbour linear plasmids corresponding to these large contigs with protein-capped termini. These linear plasmids encode a hybrid type VII/type IV secretion system but lack relaxase genes, which are typically present in mycobacterial circular plasmids. Additionally, they contain approximately 415 bp inverted repeats at the termini. Sequences of related plasmids were identified exclusively in the genomes of M. avium isolates from Japan available in public databases, suggesting a possible Asian origin. This study provides the first experimental evidence that M. avium harbours giant invertron-type linear plasmids carrying a tRNA array unit.

Several species of toxic butterflies are known, including those from the Troidini tribe of the Papilionidae, which accumulate aristolochic acid from their host plants in Aristolochiae. However, the molecular mechanisms involved in utilizing aristolochic acid remain unknown. Toxic butterflies often exhibit warning colouration to signal their toxicity to predators, a complex adaptive trait with toxin utilization. In this study, we sequenced, assembled, and annotated the genomes of 2 toxic Troidini butterflies, Pachliopta aristolochiae (312.1 Mb, 13,497 genes) and Byasa alcinous (257.6 Mb, 14,669 genes), and conducted comparative genomics to identify genes involved in toxin utilization and warning colouration. Comparative analysis across 11 species revealed 31 gene families significantly expanded and 417 genes under positive selection. Additionally, 442 genes were highly expressed in the red spots on the hindwings of P. aristolochiae. The genes shared within these lists may be involved in the formation of the complex adaptive traits of toxin utilization and warning colouration. Functional analysis using RNAi confirmed the involvement of ebony, laccase2, and tyrosine hydroxylase (TH) in warning colouration. This research marks a significant starting point in understanding the genetic basis of aristolochic acid utilization and the formation of warning colouration, providing the first list of candidate genes.

Malcolmia littorea, a member of the family Brassicaceae, is adapted to coastal and sandy environments and has become a model in studies of reproductive barriers. However, genomic resources for the species are limited. Here, with the aim of understanding the molecular mechanisms underlying key traits in M. littorea, we present a de novo genome assembly consisting of 10 chromosome-scale sequences. We employed a high-fidelity long-read sequencing technology for genome assembly. To anchor the sequences to chromosomes, we developed a single-pollen genotyping method to construct a genetic linkage map based on SNPs derived from transcriptomes of pollen grains, possessing recombinant haploid genomes. We built a genome assembly consisting of 10 chromosome-scale sequences (215 Mb in total) for M. littorea containing 30,266 predicted genes. A comparative genome analysis and gene prediction indicated that the genome of M. littorea is double the size of the Arabidopsis thaliana genome, consistent with a whole-genome duplication followed by gene subfunctionalization and/or neofunctionalization in M. littorea. This study provides a basis for research on M. littorea, an understudied species with ecological and evolutionary significance.

We present a study on amino acid composition, codon usage bias (CUB), and levels of selection driving codon usage in Sordariales fungi. We found that GC-ending codons are used more often than AT-ending codons in all Sordariales genomes, but the strength of CUB differs amongst families. The families Podosporaceae and Sordariaceae contain relatively low genome-wide levels of CUB, while the highest levels of CUB are found in Chaetomiaceae and the "BLLNS" group, a monophyletic group of 5 other Sordariales families. Based on genomic clustering, we show that Podosporaceae and Sordariaceae are more similar to each other than either of them are to any of the other groups. Comparatively, the Chaetomiaceae and BLLNS show increased natural selection driving use of specific codons, resulting in higher genome-wide CUB. We hypothesize that the higher levels of CUB in Chaetomiaceae genomes might have been caused by ecological niche specialization, versus the more generalist nature of many Sordariaceae and Podosporaceae species.

Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes, a useful model organism studied in diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a unified platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing various in silico solutions for bench biologists. This initiative led to the launch of MedakaBase (https://medakabase.nbrp.jp), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides on-demand browsing of diverse genome-wide datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3' untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase.

Salmonella enterica serovar I 4,[5],12:i:- (serovar I 4,[5],12:i:-) is one of the most frequent multidrug-resistant (MDR) Salmonella serovars associated with food-animal production globally, and strains often contain Salmonella genomic island-4 (SGI-4), an integrative conjugative element (ICE) encoding metal tolerance for copper, silver, and arsenic. Horizontal gene transfer (HGT) of SGI-4 from serovar I 4,[5],12:i:- to recipient bacteria results in enhanced metal tolerance for the transconjugants; however, the origin of transfer (oriT) for SGI-4 mobilization is unknown. In this study, the oriT within SGI-4 of MDR serovar I 4,[5],12:i:- strain USDA15WA-1 was identified by (i) cloning an internal region of SGI-4 into a non-mobilizable plasmid and demonstrating HGT to a bacterial recipient, and (ii) deleting the predicted oriT region of SGI-4 from strain USDA15WA-1 and abolishing SGI-4 transfer. Sequence similarity to oriTSGI-4 was identified in other Enterobacteriaceae, and conjugation of SGI-4 occurred from USDA15WA-1 to Salmonella serovars from Serogroups C-E as well as Escherichia coli and Citrobacter. Localization of the SGI-4 oriT enhances our understanding of a DNA region involved in HGT of an ICE in a frequent MDR Salmonella serovar, thereby providing a model to investigate HGT of SGI-4 and dissemination of metal tolerance genes in the food-animal production environment.

Chlorarachniophyte algae possess complex plastids derived from endosymbiosis between a cercozoan protist and green alga. As evidence of this event, remnant nucleus of the endosymbiont, nucleomorph, is present in the plastid intermembrane space. Chlorarachniophytes are excellent models to study genome evolution via endosymbiosis. Although the three organelle genomes of mitochondrion, plastid, and nucleomorph have been sequenced in several chlorarachniophyte species, nuclear genome information is currently limited to Bigelowiella natans. To gain insights into the genome diversity and evolution of chlorarachniophytes, we sequenced the nuclear genome of another chlorarachniophyte, Amorphochlora amoebiformis. Its size is approximately 214 Mb, which is more than twice that of B. natans. Remarkably, three-quarters of the nuclear genome encodes spliceosomal introns, indicating its highly intron-rich structure compared to other known eukaryotic genomes. Single nucleotide polymorphism analysis revealed that A. amoebiformis possessed a diploid nuclear genome, unlike the haploid genome of B. natans. Additionally, we identified organellar DNA fragments within the nuclear genome, suggesting recent DNA migration from the three organelles to the nucleus. Overall, our findings reveal that chlorarachniophyte nuclear genomes differ substantially in size, structure, and ploidy across species, and provide evidence of ongoing endosymbiotic gene transfer.

Senegalese sole is a promising European aquaculture species whose main challenge is that captive-born males (F1) are unable to reproduce in farms, hindering breeding programs. Chemical communication through the olfactory system is hypothesized to stem this issue. Although significant advancement in genomic resources has been made recently, scarce information exists on the genomic basis of olfaction, a special sensory system for demersal species like flatfish, which could play a prominent role in reproduction, social and environmental interactions. A full-length transcriptome of the olfactory rosettes including females, males, juveniles and adults, of both F1 and wild origins, was generated at the isoform-level by combining Oxford Nanopore long-read and Illumina short-read sequencing. A total of 20,670 transcripts actively expressed were identified: 13,941 known transcripts, 5,758 novel transcripts from known genes, and 971 from novel genes. Given the important role of olfaction in reproductive behaviour, we comparatively examined the expression and functional enrichment of the olfactory receptor gene families (OlfC, OR, ORA, and TAAR). Our comprehensive olfactory transcriptome of Senegalese sole provides a foundation for delving into the functional basis of this complex organ in teleost and flatfish. Furthermore, it provides a valuable resource for addressing reproductive management challenges in Senegalese sole aquaculture.