Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing

Jan and mini-Jan, a model system for potato functional genomics

Potato (Solanum tuberosum) is the third most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags relative to other major food crops due primarily to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan', which possesses all essential characteristics for facile functional genomics studies. Jan has a high level of homozygosity after seven generations of self-pollination. Jan is vigorous and highly fertile with outstanding tuber traits, high regeneration rates, and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated genes, and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two "mini-Jan" lines with compact and dwarf plant stature using CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes related to growth. Mini-Jan mutants are fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan provide an outstanding model system that can be leveraged for gene editing and functional genomics research in potato.

Genome Analysis of Anti-Phage Defense Systems and Defense Islands in Stenotrophomonas maltophilia: Preservation and Variability

Anti-phage defense systems are widespread in bacteria due to the latter continuous adaptation to infection by bacteriophages (phages). Stenotrophomonas maltophilia has a high degree of intrinsic antibiotic resistance, which makes phage therapy relevant for the treatment of infections caused by this species. Studying the array of anti-phage defense systems that could be found in S. maltophilia helps in better adapting the phages to the systems present in the pathogenic bacteria. Pangenome analysis of the available S. maltophilia strains with complete genomes that were downloaded from GenBank, including five local genomes, indicated a wide set of 72 defense systems and subsystems that varied between the strains. Seven of these systems were present in more than 20% of the studied genomes and the proteins encoded by the systems were variable in most of the cases. A total of 27 defense islands were revealed where defense systems were found; however, more than 60% of the instances of systems were found in four defense islands. Several elements linked to the transfer of these systems were found. No obvious associations between the pattern of distribution of the anti-phage defense systems of S. maltophilia and the phylogenetic features or the isolation site were found.

Centromere Landscapes Resolved from Hundreds of Human Genomes

High-fidelity (HiFi) sequencing has facilitated the assembly and analysis of the most repetitive region of the genome, the centromere. Nevertheless, our current understanding of human centromeres is based on a relatively small number of telomere-to-telomere assemblies, which have not yet captured its full diversity. In this study, we investigated the genomic diversity of human centromere higher order repeats (HORs) via both HiFi reads and haplotype-resolved assemblies from hundreds of samples drawn from ongoing pangenome-sequencing projects and reprocessed them via a novel HOR annotation pipeline, HiCAT-human. We used this wealth of data to provide a global survey of the centromeric HOR landscape; in particular, we found that 23 HORs presented significant copy number variability between populations. We detected three centromere genotypes with unbalanced population frequencies on chromosomes 5, 8, and 17. An inter-assembly comparison of HOR loci further revealed that while HOR array structures are diverse, they nevertheless tend to form a number of specific landscapes, each exhibiting different levels of HOR subunit expansion and possibly reflecting a cyclical evolutionary transition from homogeneous to nested structures and back.

Genomic data reveal a north-south split and introgression history of blood fluke (Schistosoma haematobium) populations from across Africa

The human parasitic fluke, Schistosoma haematobium hybridizes with the livestock parasite S. bovis in the laboratory, but the frequency of hybridization in nature is unclear. We analyzed 34.6 million single nucleotide variants in 162 samples from 18 African countries, revealing a sharp genetic discontinuity between northern and southern S. haematobium. We found no evidence for recent hybridization. Instead the data reveal admixture events that occurred 257-879 generations ago in northern S. haematobium populations. Fifteen introgressed S. bovis genes are approaching fixation in northern S. haematobium with four genes potentially driving adaptation. We identified 19 regions that were resistant to introgression; these were enriched on the sex chromosomes. These results (i) suggest strong barriers to gene flow between these species, (ii) indicate that hybridization may be less common than currently envisaged, but (iii) reveal profound genomic consequences of rare interspecific hybridization between schistosomes of medical and veterinary importance.

Grapevine pangenome facilitates trait genetics and genomic breeding

Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits.

Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis

Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene

The wisent (Bison bonasus) is Europe's largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of the highly conserved single copy mammalian genes which improves contiguity a thousand-fold over an existing assembly. Extended runs of homozygosity in the wisent genome compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1580 bp deletion removing the protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 sequenced samples across the Bovinae subfamily showed that the deletion is fixed in both Bison species but absent in Bos and Bubalus. The THRSP transcript is abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus, but absent in bison. This indicates that the deletion likely inactivates THRSP in bison. We show that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also demonstrate that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing.

Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies

Spatial patterns in genetic diversity are shaped by individuals dispersing from their parents and larger-scale population movements. It has long been appreciated that these patterns of movement shape the underlying genealogies along the genome leading to geographic patterns of isolation-by-distance in contemporary population genetic data. However, extracting the enormous amount of information contained in genealogies along recombining sequences has, until recently, not been computationally feasible. Here, we capitalize on important recent advances in genome-wide gene-genealogy reconstruction and develop methods to use thousands of trees to estimate per-generation dispersal rates and to locate the genetic ancestors of a sample back through time. We take a likelihood approach in continuous space using a simple approximate model (branching Brownian motion) as our prior distribution of spatial genealogies. After testing our method with simulations we apply it to Arabidopsis thaliana. We estimate a dispersal rate of roughly 60 km2/generation, slightly higher across latitude than across longitude, potentially reflecting a northward post-glacial expansion. Locating ancestors allows us to visualize major geographic movements, alternative geographic histories, and admixture. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.

Landscape of structural variants reveals insights for local adaptations in the Asian corn borer

Capturing the genetic diversity of different wild populations is crucial for unraveling the mechanisms of adaptation and establishing links between genome evolution and local adaptation. The Asian corn borer (ACB) moth has undergone natural selection during its adaptative evolution. However, structural variants (SVs), which play significant roles in these adaptation processes, have not been previously identified. Here, we constructed a multi-assembly graph pan-genome to highlight the importance of SVs in local adaptation. Our analysis revealed that the graph pan-genome contained 176.60 Mb (∼37.33%) of unique sequences. Subsequently, we performed an analysis of expression quantitative trait loci (QTLs) to explore the impact of SVs on gene expression regulation. Notably, through QTL mapping analysis, we identified the FTZ-F1 gene as a potential candidate gene associated with the traits of larval development rate. In sum, we explored the impact of SVs on the local adaptation of pests, therefore facilitating accelerated pest management strategies.

Genomes of two invasive Adelges species (hemlock woolly adelgid and pineapple gall adelgid) enable characterization of nicotinic acetylcholine receptors

Two invasive hemipteran adelgids cause widespread damage to North American conifers. Adelges tsugae (the hemlock woolly adelgid) has decimated Tsuga canadensis and Tsuga caroliniana (the Eastern and Carolina hemlocks, respectively). A. tsugae was introduced from East Asia and reproduces parthenogenetically in North America, where it can kill trees rapidly. A. abietis, introduced from Europe, makes "pineapple" galls on several North American spruce species, and weakens trees, increasing their susceptibility to other stresses. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects and the development of more selective chemical treatments could improve control methods and minimize ecological damage. Whole genome sequencing was performed on both species to aid in development of targeted pest control solutions and improve species conservation. The assembled A. tsugae and A. abietis genomes are 220.75 Mbp and 253.16 Mbp, respectively, each consisting of nine chromosomes and both genomes are over 96% complete based on BUSCO assessment. Genome annotation identified 11,424 and 14,118 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis across 29 Hemipteran species and 14 arthropod outgroups identified 31,666 putative gene families. Gene family expansions in A. abietis included ABC transporters and carboxypeptidases involved in carbohydrate metabolism, while both species showed contractions in core histone families and oxidoreductase pathways. Gene family expansions in A. tsugae highlighted families associated with the regulation of cell differentiation and development (survival motor protein, SMN; juvenile hormone acid methyltransferase JHAMT) as well as those that may be involved in the suppression of plant immunity (clip domain serine protease-D, CLIPD; Endoplasmic reticulum aminopeptidase 1, ERAP1). Among the analyzed gene families, Nicotinic acetylcholine receptors (nAChRs) maintained consistent copy numbers and structural features across species, a finding particularly relevant given their role as targets for current forestry management insecticides. Detailed phylogenetic analysis of nAChR subunits across adelgids and other ecologically important insects revealed remarkable conservation in both sequence composition and predicted structural features, providing crucial insights for the development of more selective pest control strategies.

A draft genome assembly of the reef-building coral Acropora hemprichii from the central Red Sea

Coral reef ecosystems are under threat from climate change. Thus, active interventions to spur coral conservation/restoration are critical to support reef survival, greatly informed by a molecular understanding of resilience. The genus Acropora is a species-rich and globally prevalent reef builder that has experienced dramatic declines in the Caribbean. Here we generated a draft genome of the common coral Acropora hemprichii from the central Red Sea, one of the warmest water bodies in the world. We assembled the genome using 10x Chromium sequencing with subsequent scaffolding using a reference genome and Illumina short-read sequencing contigs. The A. hemprichii genome has an assembly size of 495.6 Mb confirmed using physical size estimation, of which 247.8 Mb (50%) are repeats. The scaffold N50 is 1.38 Mb with 99.6% of BUSCO genes identified (93.7% complete, 5.9% fragmented), providing a set of 26,865 protein-coding genes. The Red Sea A. hemprichii reference genome provides a valuable resource for studies aiming to decode the genomic architecture of resilience, e.g. through comparative analyses with other Acropora genomes.

Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole-genome sequencing

Mexican wild diploid potato species are reproductively isolated from A-genome species, including cultivated potatoes; thus, their genomic relationships remain unknown. Solanum stoloniferum Schlechtd. et Bché. (2n = 4x = 48, AABB) is a Mexican allotetraploid species frequently used in potato breeding. We constructed a chromosome-scale assembly of the S. stoloniferum genome using PacBio long-read sequencing and Hi-C scaffolding technologies. The final assembly consisted of 1742 Mb, among which 745 Mb and 713 Mb were anchored to the 12 A-genome and 12 B-genome chromosomes, respectively. Using the RNA-seq datasets, we detected 20 994 and 19 450 genes in the A and B genomes, respectively. Among these genes, 5138 and 3594 were specific to the A and B genomes, respectively, and 15 856 were homoeologous, of which 18.6-25.4% were biasedly expressed. Structural variations such as large pericentromeric inversions were frequently found between the A- and B-genome chromosomes. A comparison of the gene sequences from 38 diverse genomes of the related Solanum species revealed that the S. stoloniferum B genome and Mexican diploid species, with the exception of S. verrucosum, were monophyletically distinct from the S. stoloniferum A genome and the other A-genome species, indicating that the Mexican diploid species share the B genome. The content and divergence of transposable elements (TEs) revealed recent bursts and transpositions of TEs after polyploidization. Thus, the S. stoloniferum genome has undergone dynamic structural differentiation and TE mobilization and reorganization to stabilize the genomic imbalance. This study provides new insights into polyploid evolution and the efficient use of allotetraploid species in potato breeding.

Whole-Genome Sequencing of Peribacillus frigoritolerans Strain d21.2 Isolated in the Republic of Dagestan, Russia

Pesticide-free agriculture is a fundamental pillar of environmentally friendly agriculture. To this end, there is an active search for new bacterial strains capable of synthesizing secondary metabolites and toxins that protect crops from pathogens and pests. In this study, we isolated a novel strain d21.2 of Peribacillus frigoritolerans from a soil sample collected in the Republic of Dagestan, Russia. Leveraging several bioinformatic approaches on Illumina-based whole-genome assembly, we revealed that the strain harbors certain insecticidal loci (coding for putative homologs of Bmp and Vpa) and also contains multiple BGCs (biosynthetic gene clusters), including paeninodin, koranimine, schizokinen, and fengycin. In total, 21 BGCs were predicted as synthesizing metabolites with bactericidal and/or fungicidal effects. Importantly, by applying a re-scaffolding pipeline, we managed to robustly predict MGEs (mobile genetic elements) associated with BGCs, implying high genetic plasticity. In addition, the d21.2's genome was free from genes encoding for enteric toxins, implying its safety in use. A comparison with available genomes of the Peribacillus frigoritolerans strain revealed that the strain described here contains more functionally important loci than other members of the species. Therefore, strain d21.2 holds potential for use in agriculture due to the probable manifestation of bactericidal, fungicidal, growth-stimulating, and other useful properties. The assembled genome is available in the NCBI GeneBank under ASM4106054v1.

Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events

Eukaryotic genomes are replete with satellite DNAs (satDNAs), large stretches of tandemly repeated sequences that are mostly underrepresented in genome assemblies. Here we combined nanopore long-read sequencing with a reference-guided assembly approach to generate an improved, high-quality genome assembly, TcasONT, of the model beetle Tribolium castaneum Enriched by 45 Mb in repetitive regions, the new assembly comprises almost the entire genome sequence. We use the enhanced assembly to conduct global and in-depth analyses of abundant euchromatic satDNAs. Unexpectedly, we show the extensive spread of satDNAs in gene-rich regions, including long arrays. The sequence similarity relationships between satDNA monomers and arrays indicate a recent exchange of satDNA arrays between different chromosomes. We propose a scenario of their genome dynamics characterized by repeated bursts of satDNAs spreading through euchromatin, followed by a process of elongation and homogenization of arrays. We find that suppressed recombination on the X Chromosome has no significant effect on the spread of satDNAs but the X rather tolerates the amplification of satDNAs into longer arrays. Analyses of arrays' neighboring regions show a tendency of one satDNA to be associated with transposable-like elements. Using 2D electrophoresis followed by Southern blotting, we prove Cast satDNAs' presence in the fraction of extrachromosomal circular DNA (eccDNA). We point to two mechanisms that enable this satDNA spread to occur: transposition by transposable elements and insertion mediated by eccDNA. The presence of such a large proportion of satDNA in gene-rich regions inevitably gives rise to speculation about their possible influence on gene expression.

Horizontal transfer of plasmid-like extrachromosomal circular DNAs across graft junctions in Solanaceae

The transfer of genetic material between stocks and scions of grafted plants has been extensively studied; however, the nature and frequency of the transferred material remain elusive. Here, we report a grafting system involving woody goji as the stock and herbaceous tomato as the scion, which was developed using in vitro and in vivo approaches; the results confirmed horizontal transfer of multiple nuclear DNA fragments from donor goji cells to recipient tomato cells. Tomato tissues containing goji donor DNA fragments at or near the grafting junctions had a perennial-biased anatomical structure, from which roots or shoots were regenerated. Most of the fragments were plasmid-like extrachromosomal circular DNAs (eccDNAs) present in the regenerants derived from the cells and in their asexual offspring. Plants with transferred eccDNAs in regenerated roots or shoots (designated "Go-tomato") were grown perennially and showed excellent agronomic performance. The present study provides new insights into the replication, expression, and potential function of eccDNAs in the pleiotropic traits of Go-tomato. Mobile eccDNAs offer evidence of stock-to-scion horizontal DNA transfer beyond chromosomes and organelles, thereby contributing to the molecular understanding of graft-induced genetic variation, evolution, and breeding.

Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans

TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 nonhuman primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on Chromosome 17. We find that all human copy-number variation maps to two distinct clusters located at Chromosome 17q12 and that humans are highly structurally variable at this locus, differing by as many as 20 copies and ∼1 Mbp in length depending on haplotypes. We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Last, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.

Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding

We report the construction and analysis of a new reference genome assembly for Rattus norvegicus, the laboratory rat, a widely used experimental animal model organism. The assembly has been adopted as the rat reference assembly by the Genome Reference Consortium and is named GRCr8. The assembly has employed 40× Pacific Biosciences (PacBio) HiFi sequencing coverage and scaffolding using optical mapping and Hi-C. We used genomic DNA from a male BN/NHsdMcwi (BN) rat of the same strain and from the same colony as the prior reference assembly, mRatBN7.2. The assembly is at chromosome level with 98.7% of the sequence assigned to chromosomes. All chromosomes have increased in size compared with the prior assembly and k-mer analysis indicates that the subject animal is fully inbred and that the genome is represented as a single haploid assembly. Notable increases are observed in Chromosomes 3, 11, and 12 in the prospective rDNA regions. In addition, Chr Y has increased threefold in size and is more consistent with the rat karyotype than previous assemblies. Several other chromosomes have grown by the incorporation of sizable discrete new blocks. These contain highly repetitive sequences and encode numerous previously unannotated genes. In addition, centromeric sequences are incorporated in most chromosomes. Genome annotation has been performed by NCBI RefSeq, which confirms improvement in assembly quality and adds more than 1100 new protein coding genes. PacBio Iso-Seq data have been acquired from multiple tissues of the subject animal and are released concurrently with the new assembly to aid further analyses.

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. Here, we assemble a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), including a Y chromosome of 20.96 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrects numerous genome-wide structural and base errors in previous assemblies and adds 288.5 Mb of previously unresolved regions and 446 newly assembled genes to the reference genome. We sequence the genomes of five representative goat breeds for PacBio reads, and use T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 (7.42%) in the previously unresolved regions. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the previously unresolved regions. Also, our analyses reveal a set of selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf

The high-quality genome of coconut (Cocos nucifera L.) is a crucial resource for enhancing agronomic traits and studying genome evolution within the Arecaceae family. We sequenced the Chowghat Green Dwarf cultivar, which is resistant to the root (wilt) disease, utilizing Illumina, PacBio, ONT, and Hi-C technologies to produce a chromosome-level genome of ~ 2.68 Gb with a scaffold N50 of 174 Mb; approximately 97% of the genome could be anchored to 16 pseudo-molecules (2.62 Gb). In total, 34,483 protein-coding genes were annotated; the BUSCO completeness score was 96.80%, while the k-mer completeness was ~ 87%. The assembled genome includes 2.19 Gb (81.64%) of repetitive sequences, with long terminal repeats (LTRs) constituting the most abundant class at 53.76%. Additionally, our analysis confirms two whole-genome duplication (WGD) events in the C. nucifera lineage. A genome-wide analysis of LTR insertion time revealed ancient divergence and proliferation of copia and gypsy elements. In addition, 1368 RGAs were discovered in the CGD genome. We also developed a web server 'Kalpa Genome Resource' ( http://210.89.54.198:3000/ ), to manage and store a comprehensive array of genomic data, including genome sequences, genetic markers, structural and functional annotations like metabolic pathways, and transcriptomic profiles. The web server has an embedded genome browser to analyze and visualize the genome, its genomics elements, and transcriptome data. The in-built BLAST server allows sequence homology searches against genome, annotated transcriptome & proteome sequences. The genomic dataset and the database will support comparative genome analysis and can expedite genome-driven breeding and enhancement efforts for tapping genetic gains in coconut.

Genome assembly and variant analysis of two Saccharomyces cerevisiae strains isolated from stingless bee pollen

Products from stingless bees are rich reservoirs of microbial diversity, including yeasts with fermentative potential. Previously, two Saccharomyces cerevisiae strains, JP14 and IP9, were isolated from Jataí (Tetragonisca angustula) and Iraí (Nannotrigona testaceicornis) bees, respectively, aiming at mead production. Both strains presented great osmotic and sulfite tolerance, and ethanol production, although they have a high free amino nitrogen demand. Herein, their genomes were sequenced, assembled, and annotated, and the variants were compared to the S. cerevisiae S288c reference strain. The final assembly of IP9 and JP14 presented high N50 and BUSCO scores, and more than 6430 protein-coding genes. Additionally, nQuire predicted the ploidy of IP9 as diploid, but the results were not enough to determine the ploidy of JP14. The mitochondrial genomes of IP9 and JP14 presented the same gene content as S288c but the genes were rearranged and fragmented in different patterns. Meanwhile, the genes with mutations of high impact (e.g., indels, gain of stop codon) for both yeasts were enriched for transmembrane transport, electron transfer, oxidoreductase, heme binding, fructose, mannose, and glucose transport, activities related to the respiratory chain and sugar metabolism. The IP9 strain presented copy number gains in genes related to sugar transport and cell morphogenesis; in JP14, genes were enriched for disaccharide metabolism and transport, response to reactive oxygen species, and polyamine transport. On the other hand, IP9 presented copy number losses related to disaccharide, thiamine, and aldehyde metabolism, while JP14 presented depletions related to disaccharide, oligosaccharide, asparagine, and aspartate metabolism. Notably, both strains presented a killer toxin gene, annotated from the assembling of unmapped reads, representing a potential mechanism for the control of other microorganisms population in the environment. Therefore, the annotated genomes of JP14 and IP9 presented a high selective pressure for sugar and nitrogen metabolism and stress response, consistent with their isolation source and fermentative properties.

Vibrio cholerae lineage and pangenome diversity varies geographically across Bangladesh over one year

Cholera is a diarrhoeal disease caused by Vibrio cholerae. It remains a major public health challenge in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates the others and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak season. Defining the pool of diversity during finer time scales is important because the selective pressures that impact V. cholerae - namely antibiotics and phages - are dynamic on these time scales. To study the nationwide diversity of V. cholerae, we long-read sequenced 273 V. cholerae genomes from seven hospitals over one year (2018) in Bangladesh. Four major V. cholerae lineages were identified: known lineages BD-1, BD-2a, and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, apparently outcompeting BD-2 lineages. We show that, in 2018, BD-1 was already dominant in the five northern regions, including Dhaka, consistent with an origin from India in the north. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, but nevertheless persisted throughout the year-long sampling period. Genes associated with antibiotic resistance in V. cholerae from Bangladesh in 2006 were entirely absent from all lineages in 2018-19, suggesting shifting costs and benefits of encoding these genes. Together, our results highlight the dynamic nature of the V. cholerae pangenome and the geographic structure of its lineage diversity.

Haplotype-resolved de novo assembly revealed unique characteristics of alternative lengthening of telomeres in mouse embryonic stem cells

Telomeres protect chromosome ends from DNA damage responses, and their dysfunction triggers genomic alterations like chromosome fusion and rearrangement, which can lead to cellular death. Certain cells, including specific cancer cells, adopt alternative lengthening of telomere (ALT) to counteract dysfunctional telomeres and proliferate indefinitely. While telomere instability and ALT activity are likely major sources of genomic alteration, the patterns and consequences of such changes at the nucleotide level in ALT cells remain unexplored. Here we generated haplotype-resolved genome assemblies for type I ALT mouse embryonic stem cells, facilitated by highly accurate or ultra-long reads and Hi-C reads. High-quality genome revealed ALT-specific complex chromosome end structures and various genomic alterations including over 1000 structural variants (SVs). The unique sequence (mTALT) used as a template for type I ALT telomeres showed traces of being recruited into the genome, with mTALT being replicated with remarkably high accuracy. Subtelomeric regions exhibited distinct characteristics: resistance to the accumulation of SVs and small variants. We genotyped SVs at allele resolution, identifying genes (Rgs6, Dpf3 and Tacc2) crucial for maintaining ALT telomere stability. Our genome assembly-based approach elucidated the unique characteristics of ALT genome, offering insights into the genome evolution of cells surviving telomere-derived crisis.

Comparative genomics of Plasmodium yoelii nigeriensis N67 and N67C: genome-wide polymorphisms, differential gene expression, and drug resistance

BACKGROUND

The study of rodent malaria parasites has significantly advanced our understanding of malaria parasite biology and host responses to parasite infections. There are four well-characterized rodent malaria parasite species (Plasmodium yoelii, P. chabaudi, P. berghei, and P. vinckei). Each species also has multiple strains that cause different disease phenotypes. P. yoelii nigeriensis N67C and N67, two isogenic parasites, are particularly intriguing as they differ in virulence and incite different immune responses in mice. The genome of the N67 parasite has been assembled recently, but not that of N67C. This study used PacBio HiFi sequencing data to assemble the N67C genome, compared the two genomes, and performed RNA sequencing to identify polymorphisms and differentially expressed genes (DEGs).

RESULTS

The assembled N67C parasite genome consisted of 16 scaffolds and three contigs of approximately 22.5 Mb with 100% and 96.6% completeness based on well-characterized single-copy orthologs specific to the Apicomplexa phylum and the Plasmodium genus, respectively. A comparison between the annotated N67C and N67 genomes revealed 133 single nucleotide polymorphisms (SNPs) and 75 indels. Among the polymorphic sites, an S (N67) to N (N67C) amino acid substitution at position 114 (S114N) in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) confers resistance to pyrimethamine in mice. Additionally, 60 differentially expressed single-copy genes (DEGs) were detected after comparing mRNA levels between the two parasites. Starting with the predicted and annotated 5,681 N67C and 5,749 N67 genes, we identified 4,641 orthogroups that included at least one gene from the four P. yoelii parasites (N67, N67C, 17X, and YM), whereas 758 orthogroups showed subspecies or strain-specific patterns.

CONCLUSION

The identification of polymorphic sites between the N67 and N67C genomes, along with the detection of the DEGs, may provide crucial insights into the variations in parasite drug responses and disease severity between these two isogenic parasites. The functional characterization of these genetic differences and candidate genes will deepen our understanding of disease mechanisms and pave the way for developing more effective control measures against malaria.

Fully phased genome assemblies and graph-based genetic variants of the olive flounder, Paralichthys olivaceus

The olive flounder, Paralichthys olivaceus, also known as the Korean halibut, is an economically important flatfish in East Asian countries. Here, we provided four fully phased genome assemblies of two different olive flounder individuals using high-fidelity long-read sequencing and their parental short-read sequencing data. We obtained 42-44 Gb of ~15-kb and ~Q30 high-fidelity long reads, and their assembly quality values were ~53. We annotated ~30 K genes, ~170-Mb repetitive sequences, and ~3 M 5-methylcytosine positions for each genome assembly, and established a graph-based draft pan-genome of the olive flounder. We identified 5 M single-nucleotide variants and 100 K structural variants with their genotype information, where ~13% of the variants were possibly fixed in the two Korean individuals. Based on our chromosome-level genome assembly, we also explored chromosome evolution in the Pleuronectiformes family, as reported earlier. Our high-quality genomic resources will contribute to future genomic selection for accelerating the breeding process of the olive flounder.

Nanopore ultra-long sequencing and adaptive sampling spur plant complete telomere-to-telomere genome assembly

The pursuit of complete telomere-to-telomere (T2T) genome assembly in plants, challenged by genomic complexity, has been advanced by Oxford Nanopore Technologies (ONT), which offers ultra-long, real-time sequencing. Despite its promise, sequencing length and gap filling remain significant challenges. This study optimized DNA extraction and library preparation, achieving DNA lengths exceeding 485 kb; average N50 read lengths of 80.57 kb, reaching up to 440 kb; and maximum reads of 5.83 Mb. Importantly, we demonstrated that combining ultra-long sequencing and adaptive sampling can effectively fill gaps during assembly, evidenced by successfully filling the remaining gaps of a near-complete Arabidopsis genome assembly and resolving the sequence of an unknown telomeric region in watermelon genome. Collectively, our strategies improve the feasibility of complete T2T genomic assemblies across various plant species, enhancing genome-based research in diverse fields.

Chromosome-contiguous genome for the Haecon-5 strain of Haemonchus contortus reveals marked genetic variability and enables the discovery of essential gene candidates

Millions of livestock animals worldwide are infected with the haematophagous barber's pole worm, Haemonchus contortus, the aetiological agent of haemonchosis. Despite the major significance of this parasite worldwide and its widespread resistance to current treatments, the lack of a high-quality genome for the well-defined strain of this parasite from Australia, called Haecon-5, has constrained research in a number of areas including host-parasite interactions, drug discovery and population genetics. To enable research in these areas, we report here a chromosome-contiguous genome (∼280 Mb) for Haecon-5 with high-quality models for 19,234 protein-coding genes. Comparative genomic analyses show significant genomic similarity (synteny) with a UK strain of H. contortus, called MHco3(ISE).N1 (abbreviated as "ISE"), but we also discover marked differences in genomic structure/gene arrangements, distribution of nucleotide variability (single nucleotide polymorphisms (SNPs) and indels) and orthology between Haecon-5 and ISE. We used the genome and extensive transcriptomic resources for Haecon-5 to predict a subset of essential single-copy genes employing a "cross-species" machine learning (ML) approach using a range of features from nucleotide/protein sequences, protein orthology, subcellular localisation, single-cell RNA-seq and/or histone methylation data available for the model organisms Caenorhabditis elegans and Drosophila melanogaster. From a set of 1,464 conserved single copy genes, transcribed in key life-cycle stages of H. contortus, we identified 232 genes whose homologs have critical functions in C. elegans and/or D. melanogaster, and prioritised 10 of them for further characterisation; nine of the 10 genes likely play roles in neurophysiological processes, germline, hypodermis and/or respiration, and one is an unknown (orphan) gene for which no detailed functional information exists. Future studies of these genes/gene products are warranted to elucidate their roles in parasite biology, host-parasite interplay and/or disease. Clearly, the present Haecon-5 reference genome and associated resources now underpin a broad range of fundamental investigations of H. contortus and could assist in accelerating the discovery of novel intervention targets and drug candidates to combat haemonchosis.

The tea cultivar 'Chungui' with jasmine-like aroma: From genome and epigenome to quality

'Chungui' is a newly promoted tea cultivar in China, renowned for producing oolong tea with a distinctive jasmine-like aroma. However, the genetic basis of this unique aroma remains unclear. In this study, the 'Chungui' genome, one of the most complete and well-annotated tea genomes, was assembled using PacBio HiFi reads and Hi-C sequencing. Through comparative analysis with typical jasmine flower volatiles, eight core compounds responsible for this aroma were identified. Further research revealed that the jasmine-like aroma in 'Chungui' is regulated by a coordinated mechanism involving a significant increase in chromatin accessibility and the demethylation of CHH and CHG in the promoter regions of key aroma-related genes during oolong tea processing. The study proposes that the formation of this unique aroma is driven by the synergistic effect of enhanced chromatin accessibility and reduced methylation, which together lead to the robust upregulation of genes involved in the biosynthesis of these core aroma components. These results provide a molecular foundation for understanding the unique jasmine-like aroma of 'Chungui' tea and sets the stage for future studies to explore the roles of these regulatory mechanisms in aroma formation.

A molecular mechanism for bright color variation in parrots

Parrots produce stunning plumage colors through unique pigments called psittacofulvins. However, the mechanism underlying their ability to generate a spectrum of vibrant yellows, reds, and greens remains enigmatic. We uncover a unifying chemical basis for a wide range of parrot plumage colors, which result from the selective deposition of red aldehyde- and yellow carboxyl-containing psittacofulvin molecules in developing feathers. Through genetic mapping, biochemical assays, and single-cell genomics, we identified a critical player in this process, the aldehyde dehydrogenase ALDH3A2, which oxidizes aldehyde psittacofulvins into carboxyl forms in late-differentiating keratinocytes during feather development. The simplicity of the underlying molecular mechanism, in which a single enzyme influences the balance of red and yellow pigments, offers an explanation for the exceptional evolutionary lability of parrot coloration.

Convergence and divergence of diploid and tetraploid cotton genomes

Polyploidy is an important driving force in speciation and evolution; however, the genomic basis for parallel selection of a particular trait between polyploids and ancestral diploids remains unexplored. Here we construct graph-based pan-genomes for diploid (A2) and allotetraploid (AD1) cotton species, enabled by an assembly of 50 genomes of genetically diverse accessions. We delineate a mosaic genome map of tetraploid cultivars that illustrates genomic contributions from semi-wild forms into modern cultivars. Pan-genome comparisons identify syntenic and hyper-divergent regions of continued variation between diploid and tetraploid cottons, and suggest an ongoing process of sequence evolution potentially linked to the contrasting genome size change in two subgenomes. We highlight 43% of genetic regulatory relationships for gene expression in diploid encompassing sequence divergence after polyploidy, and specifically characterize six underexplored convergent genetic loci contributing to parallel selection of fiber quality. This study offers a framework for pan-genomic dissection of genetic regulatory components underlying parallel selection of desirable traits in organisms.

Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma

Understanding the genomic diversity and functional implications of Ganoderma species is crucial for elucidating their evolutionary history and biotechnological potential. Here, we present the first pan-genomic analysis of Ganoderma spp., combining five newly sequenced genomes with ten publicly available genomes. Our comprehensive comparative study unveiled a rich genomic landscape, identifying core genes shared among all Ganoderma strains and species-specific gene sets. Additionally, we identified structural variants impacting the expression of key genes, including insights into the MSH4 gene involved in DNA repair and recombination processes, which exhibits a 440 bp insertion in the promoter region and a leucine-to-serine mutation in the gene body, potentially increasing spore production in the S3 strain. Overall, our study provides valuable insights into the genomic architecture and functional diversity of Ganoderma, paving the way for further research on its evolutionary dynamics, biotechnological applications and pharmaceutical potential.

Genomic evolution and patterns of horizontal gene transfer in Papilio

The Papilio genus, known for its ecological and phenotypic diversity, is a valuable model for evolutionary studies. This study conducted a comparative genomic analysis of 11 Papilio species, revealing species-specific gene family expansions, including the UDP-glucosyltransferase 2 gene associated with insect detoxification, particularly expanding in Papilio polyxenes. Our analysis also revealed 199 horizontal gene transfer (HGT) acquired genes from 76 microbial species, with Pseudomonadota and Bacillota as common HGT donors across these genomes. Furthermore, we examined the evolutionary patterns of nine ABC transporter subfamilies, uncovering potential links between gene family evolution and environmental adaptation. This study provides new insights into evolutionary relationships and genomic adaptations within the Papilio genus, contributing to broader butterfly evolutionary research.

Comparative Genomics Reveals Species-Specific Genes and Symbiotic Adaptations in Tricholoma matsutake

Tricholoma matsutake, a highly valued ectomycorrhizal fungus, requires a symbiotic relationship with pine trees for growth, complicating its cultivation. This study presents a comprehensive comparative genomic analysis of Tricholoma species, with a focus on T. matsutake. Genomic data from 19 assemblies representing 13 species were analyzed to identify genus-, species-, and strain-specific genes, revealing significant evolutionary adaptations. Notably, T. matsutake exhibits a higher proportion of repetitive elements compared to other species, with retrotransposons like LTR Gypsy dominating its genome. Phylogenomic analyses showed that T. matsutake forms a monophyletic group closely related to T. bakamatsutake. Gene family expansion and contraction analyses highlighted the unique evolutionary pressures on T. matsutake, particularly the loss of tryptophan-related metabolic pathways and the gain of genes related to iron ion homeostasis, which may be crucial for its adaptation to nutrient-limited environments. Additionally, the reduction in secreted proteins and carbohydrate-active enzymes reflects the host-dependent lifestyle of T. matsutake and related species. These findings enhance our understanding of the genetic and evolutionary mechanisms underlying the complex symbiotic relationships of T. matsutake, offering potential avenues for optimizing its cultivation and commercial value.

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes

Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2n = 66) and Staurotypus triporcatus (XX/XY, 2n = 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling in Apalone (Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions in Staurotypus (Kinosternidae) and Trachemys scripta (Emydidae). Furthermore, we identified a chromosome folding pattern that enables "centromere-telomere interactions" previously undetected in turtles. The combined turtle pattern of "centromere-telomere interactions" (discovered here) plus "centromere clustering" (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome.

Virulence perspective genomic research unlocks the secrets of Rhizoctonia solani associated with banded sheath blight in Barnyard Millet (Echinochloa frumentacea)

Introduction

Banded sheath blight (Bsb) disease, caused by Rhizoctonia solani, is an emerging problem in barnyard millet cultivation. One of the significant goals of pathogenomic research is to identify genes responsible for pathogenicity in the fungus.

Methods

A virulence profiling-based approach was employed and six R. solani isolates were collected from various ecological zones of India. The morphological parameters and virulence of all of the six R. solani isolates were investigated. The most virulent strain was designated as RAP2 and its genome has been sequenced, assembled, and annotated.

Results

The RAP2 genome is 43.63 megabases in size and comprises 10.95% repetitive DNA, within which 46% are retroelements, 8% are DNA transposons, and 46% are unidentified DNA. The Gene Ontology (GO) annotation of RAP2 proteins revealed that "phosphorylation", "membrane", and "ATP binding" have the highest gene enrichment in the "biological process", "cellular component" and "molecular function" domains, respectively. The genome comprises a majority of secretory proteins in the pectin lyase fold/virulence factor superfamily, which break down plant cell wall polymers to extract saccharides. The RAP2 genome is comparable to R. solani, which infects maize and rice, but it diverges further from soybean in terms of nucleotide-level genetic similarity. Orthologous clustering of RAP2 protein sequences with R. solani infecting maize, rice, and soybean yields 5606 proteins shared across all genomes. GO analysis of 25 proteins specific to the RAP2 genome found enrichment in the ethylene response, which can cause spore germination and infection in host plants.

Discussion

Interestingly, a 28-bp deletion in the RAP2 strain's cutinase domain was discovered in the cutinase protein, which might be important in the infection process, perhaps rendering the enzyme inactive or allowing the pathogen to infect barnyard millet while avoiding host defense. This study sheds light on the genetic makeup of R. solani, allowing researchers to discover critical genes related with pathogenicity as well as potential targets for fungicide development.

A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes

The application of high-throughput chromosome conformation capture (Hi-C) technology enables the construction of chromosome-level assemblies. However, the correction of errors and the anchoring of sequences to chromosomes in the assembly remain significant challenges. In this study, we developed a deep learning-based method, AutoHiC, to address the challenges in chromosome-level genome assembly by enhancing contiguity and accuracy. Conventional Hi-C-aided scaffolding often requires manual refinement, but AutoHiC instead utilizes Hi-C data for automated workflows and iterative error correction. When trained on data from 300+ species, AutoHiC demonstrated a robust average error detection accuracy exceeding 90%. The benchmarking results confirmed its significant impact on genome contiguity and error correction. The innovative approach and comprehensive results of AutoHiC constitute a breakthrough in automated error detection, promising more accurate genome assemblies for advancing genomics research.

Comparative genomics of Fusarium species causing Fusarium ear rot of maize

Fusarium ear rot (FER), caused by the fungal pathogen Fusarium verticillioides, stands as one of the most economically burdensome and pervasive diseases affecting maize worldwide. Its impact on food security is particularly pronounced due to the production of fumonisins, toxic secondary metabolites that pose serious health risks, especially for livestock. FER disease severity is complex and polygenic, with few resistance (R) genes being identified for use in breeding resistant varieties. While FER is the subject of several breeding programs, only a few studies have investigated entire populations of F. verticillioides with corresponding virulence data to better understand and characterize the pathogenomics. Here, we sequenced and compared the genomes of 50 Fusarium isolates (43 F. verticillioides and 7 other Fusarium spp.) that were used to inoculate a diverse maize population. Our objectives were to elucidate the genome size and composition of F. verticillioides, explore the variable relationship between fumonisin production and visual disease severity, and shed light on the phylogenetic relationships among the isolates. Additionally, we conducted a comparative analysis of the nucleotide variants (SNPs) and the isolates' effectoromes to uncover potential genetic determinants of pathogenicity. Our findings revealed several promising leads, notably the association of certain gene groups, such as pectate lyase, with disease severity. These genes should be investigated further as putative alleles for breeding resistant maize varieties. We suggest that, beyond validation of the alleles identified in this study, researchers validate each phenotypic dataset on an individual basis, particularly if considering fumonisin concentrations and when using diverse populations. Our study underscores the importance of genomic analysis in tackling FER and offers insights that could inform the development of resilient maize cultivars. By leveraging advances in genomics and incorporating pathogen populations into breeding programs, resistance to FER can be advanced.

MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge

The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short-read, de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target capture short-read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short-read data. MHConstructor facilitates wide-spread access to high-quality, alignment-free MHC sequence analysis.

High-quality chromosome-level genome assembly of female Artemia franciscana reveals sex chromosome and Hox gene organization

Artemia is a crustacean genus belonging to the order Anostraca in the class Branchiopoda and lives in inland hypersaline lakes. Among the genus, A. franciscana is a valuable species as a fish food in the aquaculture industry or as an aquatic model organism for toxicity tests. However, genomic data for A. franciscana remains incomplete. In this study, high-quality genome assembly at the chromosome level of female A. franciscana was conducted by combining various sequencing and assembly technologies. The final A. franciscana assembled genome was 1.27 Gb in length, containing 21 chromosomal scaffolds (>10 Mb). The scaffold N50 was 45.3 Mb, with a complete BUSCO value of 91.0 %, thereby confirming that a high-quality genome was assembled. Gene annotation shows that the A. franciscana genome contained 67.26 % of repetitive sequences, and a total of 26,923 protein-coding genes were predicted. Among the 21 chromosome-scale scaffolds, chromosome 1 was identified as a sex chromosome Z. Additionally, five contigs of putative W chromosome fragments and the candidate sex-determining genes were suggested. Ten homeobox (Hox) genes were identified in A. franciscana on the chromosome 14, which were in two subclusters with a large gap. Hox gene organizations within 13 arthropods showed that four anostracans had conserved synteny. This study provides a new female Artemia genome with sex chromosome and the first complete genomic arrangement of the Hox cluster in Anostraca. This study will be a useful genomic and genetic reference for understanding the evolution and development of A. franciscana.

Genome of Russian Snow-White Chicken Reveals Genetic Features Associated with Adaptations to Cold and Diseases

Russian Snow White (RSW) chickens are characterized by high egg production, extreme resistance to low temperatures, disease resistance, and by the snow-white color of the day-old chicks. Studying the genome of this unique chicken breed will reveal its evolutionary history and help to understand the molecular genetic mechanisms underlying the unique characteristics of this breed, which will open new breeding opportunities and support future studies. We have sequenced and made a de novo assembly of the whole RSW genome using deep sequencing (250×) by the short reads. The genome consists of 40 chromosomes with a total length of 1.1 billion nucleotide pairs. Phylogenetic analysis placed the RSW near the White Leghorn, Fayoumi, and Houdan breeds. Comparison with other chicken breeds revealed a wide pool of mutations unique to the RSW. The functional annotation of these mutations showed the adaptation of genes associated with the development of the nervous system, thermoreceptors, purine receptors, and the TGF-beta pathway, probably caused by selection for low temperatures. We also found adaptation of the immune system genes, likely driven by selection for resistance to viral diseases. Integration with previous genome-wide association studies (GWAS) suggested several causal single nucleotide polymorphisms (SNPs). Specifically, we identified an RSW-specific missense mutation in the RALYL gene, presumably causing the snow-white color of the day-old chicks, and an RSW-specific missense mutation in the TLL1 gene, presumably affecting the egg weight.

A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae

Timorese crabgrass (Digitaria radicosa) is a grass species commonly found in Southeast Asia and Oceania. Digitaria species have high intraspecific and interspecific genetic and phenotypic diversity, suggesting their potential usefulness as a genetic resource. However, as the only high-quality reference genome available is for a tetraploid Digitaria species, a reference genome of the diploid species D. radicosa would be a useful resource for genomic studies of Digitaria and Poaceae plants. Here, we present a chromosome-level genome assembly of D. radicosa and describe its genetic characteristics; we also illustrate its usefulness as a genomic resource for Poaceae. We constructed a 441.6 Mb draft assembly consisting of 61 contigs with an N50 contig length of 41.5 Mb, using PacBio HiFi long reads. We predicted 26,577 protein-coding genes, reaching a BUSCO score of 96.5%. To demonstrate the usefulness of the D. radicosa reference genome, we investigated the evolution of Digitaria species and the genetic diversity of Japanese Digitaria plants based on our new reference genome. We also defined the syntenic blocks between D. radicosa and 2 Poaceae crops, fonio and rice, and the diverse distribution of representative resistance genes in D. radicosa. The D. radicosa reference genome presented here should help elucidate the genetic relatedness of Digitaria species and the genetic diversity of Digitaria plants. In addition, the D. radicosa genome will be an important genomic resource for Poaceae genomics and crop breeding.

Genome sequence of Heterobasidion occidentale, a fungus that causes annosus root and butt rot among conifer trees in North America

We report an annotated draft genome of Heterobasidion occidentale, a fungus (Basidiomycota, Agaricomycetes) that has pathogenic and saprophytic lifestyles. This fungus belongs to the H. annosum (Fr.) Bref. sensu lato species complex that comprises several root rot pathogens. Heterobasidion occidentale causes annosus root and butt rot primarily in true fir (Abies spp.) and spruce (Picea spp.) species throughout western North America.

Genomic diversity and evolution of the Hawaiian Islands endemic Kokia (Malvaceae)

Island species are highly vulnerable due to habitat destruction and their often small population sizes with reduced genetic diversity. The Hawaiian Islands constitute the most isolated archipelago on the planet, harboring many endemic species. Kokia is an endangered flowering plant genus endemic to these islands, encompassing 3 extant and 1 extinct species. Recent studies provided evidence of unexpected genetic diversity within Kokia. Here, we provide high-quality genome assemblies for all 3 extant Kokia species, including an improved genome for Kokia drynarioides. All 3 Kokia genomes contain 12 chromosomes exhibiting high synteny within and between Kokia and the sister taxon Gossypioides kirkii. Gene content analysis revealed a net loss of genes in K. cookei compared to other species, whereas the gene complement in K. drynarioides remains stable and that of Kokia kauaiensis displays a net gain. A dated phylogeny estimates the divergence time from the last common ancestor for the 3 Kokia species at ∼1.2 million years ago (mya), with the sister taxa (K. cookei + K. drynarioides) diverging ∼0.8 mya. Kokia appears to have followed a stepping-stone pattern of colonization and diversification of the Hawaiian archipelago, likely starting on low or now submerged older islands. The genetic resources provided may benefit conservation efforts of this endangered endemic genus.

Comparative genomics unravels a rich set of biosynthetic gene clusters with distinct evolutionary trajectories across fungal species (Termitomyces) farmed by termites

The use of compounds produced by hosts or symbionts for defence against antagonists has been identified in many organisms, including in fungus-farming termites (Macrotermitinae). The obligate mutualistic fungus Termitomyces plays a pivotal role in plant biomass decomposition and as the primary food source for these termites. Despite the isolation of various specialized metabolites from different Termitomyces species, our grasp of their natural product repertoire remains incomplete. To address this knowledge gap, we conducted a comprehensive analysis of 39 Termitomyces genomes, representing 21 species associated with members of five termite host genera. We identified 754 biosynthetic gene clusters (BGCs) coding for specialized metabolites and categorized 660 BGCs into 61 biosynthetic gene cluster families (GCFs) spanning five compound classes. Seven GCFs were shared by all 21 Termitomyces species and 21 GCFs were present in all genomes of subsets of species. Evolutionary constraint analyses on the 25 most abundant GCFs revealed distinctive evolutionary histories, signifying that millions of years of termite-fungus symbiosis have influenced diverse biosynthetic pathways. This study unveils a wealth of non-random and largely undiscovered chemical potential within Termitomyces and contributes to our understanding of the intricate evolutionary trajectories of biosynthetic gene clusters in the context of long-standing symbiosis.

Whole-genome sequencing of Klebsiella pneumoniae MDR circulating in a pediatric hospital setting: a comprehensive genome analysis of isolates from Guayaquil, Ecuador

BACKGROUND

Klebsiella pneumoniae is the major cause of nosocomial infections worldwide and is related to a worsening increase in Multidrug-Resistant Bacteria (MDR) and virulence genes that seriously affect immunosuppressed patients, long-stay intensive care patients, elderly individuals, and children. Whole-Genome Sequencing (WGS) has resulted in a useful strategy for characterizing the genomic components of clinically important bacteria, such as K. pneumoniae, enabling them to monitor genetic changes and understand transmission, highlighting the risk of dissemination of resistance and virulence associated genes in hospitals. In this study, we report on WGS 14 clinical isolates of K. pneumoniae from a pediatric hospital biobank of Guayaquil, Ecuador.

RESULTS

The main findings revealed pronounced genetic heterogeneity among the isolates. Multilocus sequencing type ST45 was the predominant lineage among non-KPC isolates, whereas ST629 was found more frequently among KPC isolates. Phylogenetic analysis suggested local transmission dynamics. Comparative genomic analysis revealed a core set of 3511 conserved genes and an open pangenome in neonatal isolates. The diversity of MLSTs and capsular types, and the high genetic diversity among these isolates indicate high intraspecific variability. In terms of virulence factors, we identified genes associated with adherence, biofilm formation, immune evasion, secretion systems, multidrug efflux pump transporters, and a notably high number of genes related to iron uptake. A large number of these genes were detected in the ST45 isolate, whereas iron uptake yersiniabactin genes were found exclusively in the non-KPC isolates. We observed high resistance to commonly used antibiotics and determined that these isolates exhibited multidrug resistance including β-lactams, aminoglycosides, fluoroquinolones, quinolones, trimetropins, fosfomycin and macrolides; additionally, resistance-associated point mutations and cross-resistance genes were identified in all the isolates. We also report the first K. pneumoniae KPC-3 gene producers in Ecuador.

CONCLUSIONS

Our WGS results for clinical isolates highlight the importance of MDR in neonatal K. pneumoniae infections and their genetic diversity. WGS will be an imperative strategy for the surveillance of K. pneumoniae in Ecuador, and will contribute to identifying effective treatment strategies for K. pneumoniae infections in critical units in patients at stratified risk.

Assembly and comparative analysis of the mitochondrial genome in diploid potatoes

KEY MESSAGE

We report the mitochondrial genome of 39 diploid potatoes and identify a candidate ORF potentially linked to cytoplasmic male sterility in potatoes. Potato (Solanum tuberosum L.) holds a critical position as the foremost non-grain food crop, playing a pivotal role in ensuring global food security. Diploid potatoes constitute a vital genetic resource pool, harboring the potential to revolutionize modern potato breeding. Nevertheless, diploid potatoes are relatively understudied, and mitochondrial DNA can provide valuable insights into key potato breeding traits such as CMS. In this study, we examine and assemble the mitochondrial genome evolution and diversity of 39 accessions of diploid potatoes using high-fidelity (HiFi) sequencing. We annotated 54 genes for all the investigated accessions, comprising 34 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. Our analyses revealed differences in repeats sequences between wild and cultivated landraces. To understand the evolution of diploid maternal lineage inheritance, we conducted phylogenetic analysis, which clearly distinguished mitochondrial from nuclear gene trees, further supporting the evidence-based of clustering between wild and cultivated landraces accessions. Our study discovers new candidate ORFs associated with CMS in potatoes, including ORF137, which is homologous to other CMS in Solanaceae. Ultimately, this work bridges the gap in mitochondrial genome research for diploid potatoes, providing a steppingstone into evolutionary studies and potato breeding.

Sorlinia euscelidii gen. nov., sp. nov., a novel acetic acid bacterium isolated from the leafhopper Euscelidius variegatus (Hemiptera: Cicadellidae)

Acetic acid bacteria - belonging to the Acetobacteraceae family - are found in the gut of many sugar-feeding insects. In this study, six strains have been isolated from the hemipteran leafhopper Euscelidius variegatus. While they exhibit high 16S rRNA gene sequence similarities to uncultured members of the Acetobacteraceae family, they could not be unequivocally assigned to any particular type species. Considering the clonality of the six isolates, the EV16PT strain was used as a representative of this group of isolates. The genome sequence of EV16PT is composed of a 2.388 Mbp chromosome, with a DNA G+C content of 57 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis indicate that EV16PT forms a monophyletic clade with the uncultivated endosymbiont of Diaphorina citri, the Candidatus Kirkpatrickella diaphorinae. Such a phylogenetic clade is positioned between those of Asaia-Swaminathania and Kozakia. The genomic distance metrics based on gene and protein sequences support the proposal that EV16PT is a new species belonging to a yet-undescribed genus. It is a rod-shaped Gram-stain-negative bacterium, strictly aerobic, non-motile, non-spore-forming, showing optimal growth without salt (NaCl) at 30 °C and pH of 6-7. The major quinone is Q10, and the dominant cellular fatty acids (>10%) are C18:l ω7c, C19 : 0 cyclo ω6c, C16 : 0 and C19 : 1 2OH. The polar lipid profile comprises diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine, along with unidentified aminophospholipids, glycophospholipids, aminolipids and lipids. Based on a polyphasic approach, including phylogenetic, phylogenomic, genome relatedness, phenotypic and chemotaxonomic characterisations, EV16PT (= KCTC 8296T, = DSM 117028T) is proposed as a representative of a novel species in a novel genus with the proposed name Sorlinia euscelidii gen. nov., sp. nov., in honour of Prof. Claudia Sorlini, an Italian environmental microbiologist at the University of Milan who inspired the research on microbial diversity, including symbiosis in plants and animals.

Transposable elements in Drosophila montana from harsh cold environments

BACKGROUND

Substantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular and structural effects. Yet, our knowledge on the role of TEs in adaptation to extreme climates is still at its infancy. The availability of long-read sequencing has opened up the possibility to identify and study potential functional effects of TEs with higher precision. In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates.

RESULTS

Using the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographically distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11-13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. Finally, we detected TEs nearby fixed and polymorphic inversion breakpoints.

CONCLUSIONS

Our research revealed a significant number of newly identified TE consensus sequences in the genome of D. montana, suggesting that non-model species should be studied to get a comprehensive view of the TE repertoire in Drosophila species and beyond. Genome annotations with the new D. montana library allowed us to identify TEs located nearby cold tolerant genes, and present at high population frequencies, that contain regulatory regions and are thus good candidates to play a role in D. montana cold stress response. Finally, our annotations also allow us to identify for the first time TEs present in the breakpoints of three D. montana inversions.

Chromosome-level genome assembly and comparative genomics shed light on Helicoverpa assulta ecology and pest management

BACKGROUND

The Oriental tobacco budworm, Helicoverpa assulta, a specialist herbivorous insect that exclusively feeds on plants of the Solanaceae family, causes considerable damage to crops, such as tobacco and hot pepper. The absence of a genome sequence for this species hinders further research on its pest management and ecological adaptation.

RESULTS

Here, we present a high-quality chromosome-level genome of a Korean strain of H. assulta (Pyeongchang strain, K18). The total assembly spans 424.4 Mb with an N50 length of 14.54 Mb and 37% GC content. The assembled genome (ASM2961881v1) comprises 31 chromosomes, similar to other congeneric generalist species including H. armigera and H. zea. In terms of genomic assembly quality, the complete BUSCOs and repeat content accounted for 98.3% and 33.01% of the genome, respectively. Based on this assembly, 19 485 protein-coding genes were predicted in the genome annotation. A comparative analysis was conducted using the identified number of protein-coding genes in H. armigera (24154) and H. zea (23696). Out of the 19 485 predicted genes, 137 genes in 15 orthogroups were found to have expanded significantly in H. assulta, while 149 genes in 95 orthogroups contracted rapidly.

CONCLUSION

This study revealed specific gene expansions and contractions in H. assulta compared to those in its close relatives, indicating potential adaptations related to its specialized feeding habits. Also, the comparative genome analysis provides valuable insights for the integrated pest management of H. assulta and other globally significant pests in the Heliothinae subfamily. © 2024 Society of Chemical Industry.

Biparental graph strategy to represent and analyze hybrid plant genomes

Hybrid plants are found extensively in the wild, and they often demonstrate superior performance of complex traits over their parents and other selfing plants. This phenomenon, known as heterosis, has been extensively applied in plant breeding for decades. However, the process of decoding hybrid plant genomes has seriously lagged due to the challenges associated with genome assembly and the lack of appropriate methodologies for their subsequent representation and analysis. Here, we present the assembly and analysis of 2 hybrids, an intraspecific hybrid between 2 maize (Zea mays ssp. mays) inbred lines and an interspecific hybrid between maize and its wild relative teosinte (Z. mays ssp. parviglumis), utilizing a combination of PacBio High Fidelity sequencing and chromatin conformation capture sequencing data. The haplotypic assemblies are well phased at chromosomal scale, successfully resolving the complex loci with extensive parental structural variations (SVs). By integrating into a biparental genome graph, the haplotypic assemblies can facilitate downstream short-read-based SV calling and allele-specific gene expression analysis, demonstrating outstanding advantages over a single linear genome. Our work offers a comprehensive workflow that aims to facilitate the decoding of numerous hybrid plant genomes, particularly those with unknown or inaccessible parentage, thereby enhancing our understanding of genome evolution and heterosis.

The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation

BACKGROUND

Understanding the molecular basis of sport mutations in fruit trees has the potential to accelerate generation of improved cultivars.

RESULTS

For this, we analyzed the genome of the apple tree that developed the RubyMac phenotype through a sport mutation that led to the characteristic fruit coloring of this variety. Overall, we found 46 somatic mutations that distinguished the mutant and wild-type branches of the tree. In addition, we found 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) that also distinguished the two parts of the tree. Approximately 20% of the mutations were specific to individual cell lineages, suggesting that they originated from the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC =  > AT transitions while the gene conversions showed the opposite bias for AT =  > GC transitions, suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a somatic mutation, we found that some of them in regions of the genome that were recently associated with natural variation in fruit coloration.

CONCLUSION

Our analysis revealed insights in the characteristics of somatic change, which not only included de novo mutations but also gene conversions. Some of these somatic changes displayed strong candidate mutations for the change in fruit coloration in RubyMac.