GenomeScope: fast reference-free genome profiling from short reads

Molecular and genomic insights into the pathogenicity of Sarocladium zeae causing maize stalk rot disease

Post-flowering stalk rot (PFSR) of maize has been traditionally associated with Fusarium verticillioides. Conversely, this study reveals Sarocladium zeae as a new phytopathogen responsible for the disease. This research was conducted to gain a comprehensive understanding of S. zeae by investigating its pathogenic mechanisms, profiling its metabolome, and deciphering its genomic characteristics. Maize stalks displaying stalk rot symptoms were collected from various regions of India. S. zeae was isolated and characterized using ITS and TEF-1α sequencing. Cultures of S. zeae exhibited slower growth on PDA medium compared to F. verticillioides, which dominated due to its rapid growth rate. Pathogenicity was confirmed through a toothpick inoculation assay. The symptoms induced by S. zeae was characterized by powdery, dry, pale brown-black discoloration, were distinct from the typical dark-brown lesions of Fusarium stalk rot. Enzymatic assays revealed increased activity of β-glucosidase, cellulase, and pectate lyase in infected stalks, while qPCR analysis showed the upregulation of endoglucanase and β-glucosidase genes in infected stalks underscored the critical roles of cellulase and β-glucosidase in pathogenicity Metagenomic analysis identified S. zeae as the predominant species in infected stalk samples. Genome assembly revealed the pathogen's complete genetic repertoire, including genes encoding effector proteins and CAZymes involved in cell wall degradation. Moreover, we have demonstrated that the S. zeae as a causal agent of maize stalk rot and further shedding light on its transition from an endophytic to a pathogenic lifestyle. Taken together, this research represents the first report to attribute maize stalk rot to S. zeae and to present its complete genome assembly, significantly advancing the understanding of its biology and pathogenic potential.

A PCR primer design method for identifying spider mite species using k-mer counting

Using PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candidate sequences (i.e., unpaired primers that were specific to a single species) from RNA-Seq data sets of 19 species of spider mites (Acari, Tetranychidae). Using k-mer counting, we obtained between 257 and 48,621 species-specific unpaired primer candidates for the 19 species. We then manually obtained a second primer that was also species-specific. The primer pairs were then confirmed to work in the target species and not to work in the non-target species. Finally, species-specific primer pairs were obtained for 17 of the 19 species tested. Such species-specific primers may be used for practical species discrimination by optimizing multiplex PCR. Our primer design method is expected to be applicable to other taxa.

Chromosome-level genome assembly and annotation of the maize weevil (Sitophilus zeamais Motschulsky)

The maize weevil, Sitophilus zeamais Motschulsky, is one of the most destructive pests of stored grains worldwide, posing a significant threat to global food security. To better understand the biology, resistance mechanism, and adaptive evolution of this species, we presented a high-quality chromosome-level genome assembly of S. zeamais using PacBio sequencing and Hi-C technologies. The size of the final assembled genome was 693.21 Mb with scaffold N50 of 61.03 Mb, and 631.97 Mb were successfully anchored into 11 pseudochromosomes. In total, 15,161 protein-coding genes were annotated, of which 98.89% obtained functional descriptions. Additionally, 377.50 Mb of sequences were identified as repeat elements, accounting for 54.46% of the genome. BUSCO analysis revealed a high level of completeness in both the genome assembly and annotation, with scores of 98.17% and 97.22%, respectively. The chromosome-level genome of S. zeamais provides valuable genomic insights that deepen our understanding of the evolution and ecology of Sitophilus species, while also contributing to the development of targeted and innovative control strategies for stored-product pests.

Haplotype-resolved telomere-to-telomere genome assembly of the dikaryotic fungus pathogen Rhizoctonia cerealis

Rhizoctonia cerealis, the causal agent of sharp eyespot, is a highly destructive pathogen of wheat. Despite its global importance, the genetic and molecular mechanisms underlying virulence of R. cerealis remain poorly understood. R. cerealis is a dikaryotic organism and the haplotype phase has been isolated. Based on the PacBio HiFi, Oxford Nanopore, and Hi-C platforms, we assembled the first high quality telomere-to-telomere (T2T) haplotype-resolved genome of R. cerealis, with sizes of 41.50 and 41.05 Mb, and N50 sizes of 2.67 and 2.42 Mb, respectively. High consensus quality values of 57.75 and 57.09 for the two haplotypes validated the accuracy of the assembly. The assembly achieved R-AQI and S-AQI scores of 92.5 and 100, respectively, both indicating reference-level quality. A total 25,353 protein coding genes were predicted for the two haplotypes with a BUSCO score of 96.7%. The genome assembly will serve as the foundation for further research on allele-specific expression, genetic variation and evolution of R. cerealis.

Genomic insights into genome-wide heterozygosity and its impact on walnut adaptive evolution and improvement

Walnut (Juglans regia L.), an important woody oil plant, is cultivated globally and has a prominent position in the world's major nuts. Heterozygosity enriches plant genetic diversity by providing a wider array of gene combinations, significantly enhancing their adaptability to the environment and consequently improving their survival ability. In this study, we found that the heterozygosity rate was significantly correlated with 21 traits. Heterogeneity rate showed the strongest positive correlation with yield and nutrition, while it showed the most significant negative correlation with tree height and precocity. Among these, 13 traits showed positive correlations, the remaining 8 traits exhibited negative correlations. We conducted an in-depth study on the characteristics of walnut whole-genome heterozygosity. By using the GWAS based on the heterozygosity rate, we successfully identified 11 significant loci and 4 candidate genes. In the analysis of local heterozygosity rate by GWAS, it was found that 63.8% exhibited trans-acting and 36.2% exhibited cis-acting. In addition, with the help of genomic residual heterozygotes, we enriched functional genes from 44 Pfam families related to growth regulation and development. Finally, it is worth mentioning that during the process of walnut improvement, we observed an increase in the heterozygosity rate of genes related to the flowering time. It is speculated that a higher level of whole-genome heterozygosity can enhance the environmental adaptability of plants and improve their growth performance. The results of this study may provide assistance for optimizing the breeding strategies of walnuts.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01572-2.

Long-distance seasonal migration to the tropics promotes genetic diversity but not gene flow in boreal birds

Differences in life history can cause co-distributed species to evolve contrasting population genetic patterns, even as they occupy the same landscape. In high-latitude animals, evolutionary processes may be especially influenced by long-distance seasonal migration, a widespread adaptation to seasonality. Although migratory movements are intuitively linked to dispersal and therefore promotion of gene flow, their evolutionary genetic consequences remain poorly understood. Using ~1,700 genomes from 35 co-distributed boreal-breeding bird species that differ in non-breeding latitude and thus migration distance, we find that most long-distance migrants unexpectedly exhibit spatial genetic structure, despite their strong movement propensity. This result suggests evolutionary effects of philopatry-the tendency of many migrants to return to the same breeding site year after year, resulting in restricted dispersal. We further demonstrate that migration distance and genetic diversity are strongly positively correlated in our study species. This striking relationship suggests that the adaptive seasonal shifts in biogeography inherent to long-distance migration may enhance population stability, preserving genetic diversity in long-distance migrants relative to shorter-distance migrants that winter in harsher conditions at higher latitudes. Our results suggest that the major impact of long-distance seasonal migration on population genetic evolution occurs through promotion of demographic stability, rather than facilitation of dispersal.

A well-annotated genome of Apium graveolens var. dulce cv. Challenger, a celery with resistance to Fusarium oxysporum f. sp. apii race 2

Celery (Apium graveolens var. dulce) production can be limited by the fungal pathogen Fusarium oxysporum f. sp. apii (Foa), particularly at temperatures above 22°C. Because celery has a narrow genetic base, an intraspecific admixture of Apium graveolens was developed into cv. Challenger, which is resistant to Foa race 2, the causal agent of Fusarium yellows, but susceptible to Foa race 4, a relatively unrelated causal agent of Fusarium wilt. We assembled a high-quality, chromosome-level physical map of Challenger with 40 464 RNA-based, protein-coding gene models in 3.3 Gbp and anchored it with a genetic map. Although there is high gene density and higher recombination at the ends of the chromosomes, an average of 56% of the genes/chromosome are in lower recombination zones (<0.025 cM/Mb). We identified Challenger's nucleotide-binding and leucine-rich repeat receptors (NLRs) and pattern recognition receptors (PRRs), the two gene families that encode most resistance (R) genes. In three treatment groups (mock-infested or infested with either Foa race 2 or race 4), 243 NLRs and 445 PRRs were quantified in the celery crowns via Quant-Seq 3' mRNA-Seq (Tag-Seq). We compared the genomes of Challenger with that of the previously published cv. Ventura, which is moderately susceptible to Foa race 2. We present a toolbox for genome-assisted breeding for celery that includes annotated gene models, a protocol for genotype-by-sequencing, documentation of the expression of NLRs and PRRs, and a straightforward strategy for introgressing selected NLR superclusters, 83% of which are in higher recombination regions.

Chromosome-level genome assembly of Sambus kanssuensis (Coleoptera: Buprestidae)

Sambus kanssuensis Ganglbauer, 1890 (Coleoptera: Buprestidae), distributed in Gansu and Sichuan Provinces of China, is a phytophagous pest that feeds on the toxic plant Buddleja. However, the genomic resources of this beetle remain unknown, which impedes the understanding of its ecological adaptations. Consequently, this study presents a complete, well-assembled, and annotated genome of S. kanssuensis. The assembled results indicate a genome size of 312.42 Mb, comprising 206 scaffolds, with an N50 of 34.04 Mb; 98.68% of the assembly sequences were anchored to 11 chromosomes, including one sex chromosome. The genome contains 12,723 protein-coding genes, of which 11,977 have been annotated. BUSCO analysis revealed that the completeness of the chromosome-level genome is 97.9%. This chromosome-level genome provides valuable data for further investigations into detoxification mechanisms, ecological adaptations, population genetics, and the evolution of Buprestidae.

Chromosome-level genome assemblies of Verpa bohemica and Verpa conica

Verpa, commonly known as "early morel" or "false morel", plays an important ecological role and offers considerable economic and medicinal potential. Despite their significance, research on Verpa species, particularly V. bohemica and V. conica, remains limited. In this study, we assembled high-quality sub-chromosomal genomes of six Verpa strains using Nanopore and Illumina sequencing, with average sizes of 44.38 Mb for V. bohemica and 45.40 Mb for V. conica. Specifically, the assemblies of V. bohemica strain 21108 and V. conica strain 21120 were anchored to 26 and 25 chromosomes with Hi-C technologies, respectively. The consensus quality value (QV) of both V. bohemica and V. conica exceeded 40. In addition, an average of 11,024 and 11,052 protein-coding genes were identified for V. bohemica and V. conica, respectively, with BUSCO completeness scores ranging from 98.71% to 99.24%. Overall, these reported genomes will provide valuable genomic resources for the evolution and ecological roles research of Verpa.

A chromosomal-level genome assembly of Araneus marmoreus Schenkel, 1953 (Araneae: Araneidae)

The marbled orb-weaver spider, Araneus marmoreus (Araneae: Araneidae), is distinguished by its unique inflated, pumpkin-like abdomen. Numerous genome studies have been conducted on Araneidae species, providing insights into their unique biological traits. However, studies on A. marmoreus remain limited, despite its ecological significance and intriguing morphology. The lack of a high-quality reference genome has further hindered in-depth exploration of its evolutionary biology and ecological dynamics. Here, we present a chromosome-level genome assembly for A. marmoreus, generated using a combination of Illumina, PacBio, and Hi-C sequencing technologies. The assembled genome is 2.39 Gb in size, comprising 13 chromosomes, with a scaffold N50 of 181.8 Mb and a contig N50 of 721.3 kb. The assembly achieved a BUSCO completeness score of 97.1% (n = 2,934), including 91.0% complete and single-copy BUSCOs and 6.1% complete and duplicated BUSCOs. Repetitive sequences accounted for 59.25% of the genome, and 23,381 protein-coding genes were annotated. This high-quality genome provides a valuable resource for advancing research into the evolutionary genomics and ecological dynamics of A. marmoreus.

De-novo assembly and comparative analysis of the complete mitogenome of traditional Chinese medicine Strobilanthes sarcorrhiza

BACKGROUND

Strobilanthes sarcorrhiza is a traditional medicinal plant known for its heat-clearing and kidney-nourishing properties. While its plastid genome has been reported, there is a scarcity of genetic information regarding its mitogenome, leading to unclear phylogenetic relationships. We sequenced and assembled the complete its mitogenome and conducted a series of genetic analyses in conjunction with the plastid genome to gain a better understanding of the species' genetic background.

RESULTS

The mitogenome comprised a linear structure spanning 617,134 bp. It included 35 protein-coding genes (PCGs), 19 transfer RNAs (tRNAs), and 3 ribosomal RNAs (rRNAs) that have been annotated. Additionally, 122 simple sequence repeats (SSRs) and 25 tandem repeats were identified. A total of 1,482 pairs of dispersed repeats were detected, which account for 17.58% of the entire mitogenome. Furthermore, 37 migration fragments between the mitochondrial and plastid genomes were discovered, consisting of 5 complete PCGs, 7 tRNAs, and 1 rRNA. Based on the analysis of 38 mitogenomes and 46 plastid genomes, the evolutionary relationship and phylogenetic position of S. sarcorrhiza were elucidated.

CONCLUSIONS

This study has, for the first time, provided insights into the mitochondrial genomic characteristics of S. sarcorrhiza and clarified its phylogenetic position. These findings offered significant insights for the future identification and classification of this genus, as well as for the genetic breeding of medicinal plants.

Chromosome-scale whole genome assembly and annotation of the Jamaican field cricket Gryllus assimilis

Gryllus assimilis, commonly known as Jamaican field cricket, is an edible insect with significant economic value in sustainable food production. Despite its importance, a high-quality reference genome of G. assimilis has not yet been published. Here, we report a chromosome-level reference genome of G. assimilis based on Oxford Nanopore Technologies (ONT) sequencing, Illumina sequencing, and Hi-C technologies. The assembled genome has a total length of 1.60 Gbp with a scaffold N50 of 102 Mbp, and 96.80% of the nucleotides was assigned to 15 chromosome-scale scaffolds. The assembly completeness was validated using BUSCO, achieving 99.5% completeness against the arthropoda database. We predicted 27,645 protein-coding genes, and 825 Mb repetitive elements were annotated in the reference genome. This reference genome of G. assimilis can provide a basis for the subsequent development of genomic resources, offering insights for future functional genomic studies, comparative genomics, and DNA-informed breeding of this species.

A telomere-to-telomere genome assembly of Camellia nitidissima

Camellia nitidissima is the model species of the Camellia sect. Chrysantha Chang, the only lineage within the genus Camellia known to produce golden-yellow flowers. This species holds high aesthetic, germplasm and medical value. Unfortunately, due to excessive collection and habitat loss, C. nitidissima is classified as a critically endangered plant. In this study, we assembled a telomere-to-telomere (T2T) genome of C. nitidissima by incorporating PacBio HiFi and Hi-C data. The assembled genome consisted of 15 pseudo-chromosomes, with a total size estimated to be 2.72 Gb. The GC content and repetitive sequences occupied 38.05% and 84.38% of the assembled genome, respectively. In total, 35,701 protein-coding genes were annotated. Multiple evaluation methods confirmed the contiguity (contig N50: 81.74 Mb), completeness (BUSCOs: 98.80%) and high LTR Assembly Index (LAI: 14.57) of the genome. This high-quality T2T genome will provide valuable insights into the genomic characteristics of C. nitidissima and facilitate conservation efforts as well as functional genomic studies in Camellia sect. Chrysantha species.

Chromosome-level genome assembly of the parasitoid wasp Aenasius arizonensis

Aenasius arizonensis is an important solitary endoparasitoid successfully used for biocontrol of cotton mealybug. However, lacking genomic resources has limited molecular-level investigations. Our exploration produced a superior genomic assembly of A. arizonensis from the chromosome level by combining MGISEQ short reads, Hi-C scaffolding, and PacBio Revio sequencing techniques. The genome measured 398.69 Mb, including a contig N50 of 4.73 Mb, a BUSCO completeness level of 97.07%, and a scaffold N50 of 35.96 Mb. Hi-C data were further utilized cluster and anchor 98.66% of the genome sequences into 11 chromosomes. Approximately, 165.90 Mb, representing about 41.61% of the genome, was identified as repeat elements. Non-coding sequence annotation identified 171 rRNAs, 117 small RNAs, 331 regulatory RNAs, and 872 tRNAs. Genome annotation reveals 11,727 protein-coding genes, with 10,842 (92.45%) genes functionally annotated. In summary, our chromosome-level genome assembly serves as a significant resource for advancing research on Encyrtidae parasitoids.

Genomic structure of yellow lupin (Lupinus luteus): genome organization, evolution, gene family expansion, metabolites and protein synthesis

Yellow lupin (Lupinus luteus) gives valuable high-quality protein and has good sustainability due to its ability in nitrogen fixation and exudation of organic acids, which reduces the need for chemical-based phosphate fertilization in acid soils. However, the crop needs further improvements to contribute in a major way to sustainable agriculture and food security.In this study, we present the first chromosome-level genome assembly of L. luteus. The results provide insights into its genomic organization, evolution, and functional attributes. Using integrated genomic approaches, we unveil the genetic bases governing its adaptive responses to environmental stress, delineating the intricate interplay among alkaloid biosynthesis, mechanisms of pathogen resistance, and secondary metabolite transporters. Our comparative genomic analysis of closely related species highlights recent speciation events within the Lupinus genus, exposing extensive synteny preservation alongside notable structural alterations, particularly chromosome translocations. Remarkable expansions of gene families implicated in terpene metabolism, stress responses, and conglutin proteins were identified, elucidating the genetic basis of L. luteus' superior nutritional profile and defensive capabilities. Additionally, a diverse array of disease resistance-related (R) genes was uncovered, alongside the characterization of pivotal enzymes governing quinolizidine alkaloid biosynthesis, thus shedding light on the molecular mechanisms underlying "bitterness" in lupin seeds.This comprehensive genomic analysis serves as a valuable resource to improve this species in terms of resilience, yield, and seed protein levels to contribute to food and feed to face the worldwide challenge of sustainable agriculture and food security.

Haplotype-resolved genome assembly provides insights into the genetic basis of green peach aphid resistance in peach

Green peach aphid (GPA) is one of the most destructive pests of peach, threatening both growth and fruit quality. However, the mechanism underlying GPA resistance remains unclear. Here, we performed haplotype-resolved genome assembly of a GPA-resistant cultivar and identified an allele-specific expressed gene, PpNLR1, responsible for the GPA-resistant trait. A genome-wide association study (GWAS) revealed a functional 20-bp insertion or deletion (indel) in the PpNLR1 promoter, which co-segregated with the GPA-resistant trait and directly influenced promoter activity. Furthermore, jasmonate (JA) signaling, activated during GPA infestation, induced the transcription of PpERF109. This transcription factor specifically bound to the "CAAGT" motif within the GWAS-identified 20-bp insertion of the PpNLR1 promoter, resulting in allele-specific expression (ASE). Functional validation of the two alleles (PpNLR1-Hap1 and PpNLR1-Hap2) in both peach and Arabidopsis demonstrated their role in aphid resistance. Additionally, two GPA salivary proteins were identified as effectors, triggering reactive oxygen species (ROS) and activating the peach immune system in conjunction with the PpNLR1 protein. Comparative genomics and phylogenetic analysis indicated that an ∼53.6-kb genomic variation surrounding PpNLR1 underwent negative selection during peach evolution. In conclusion, the JA-mediated PpERF109-PpNLR1 module and GPA effector proteins significantly contribute to GPA resistance in peach. The novel haplotype-resolved genome assembly and identified key genes provide valuable resources for future genomic research and GPA resistance breeding in peach.

New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis

BACKGROUND

Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.

RESULTS

Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.

CONCLUSIONS

Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.

Mapping-based genome size estimation

While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estimations. An alternative approach to estimate the genome size based on high contiguity assemblies and read mappings is presented here. Analyses of Arabidopsis thaliana and Beta vulgaris data sets are presented to show the impact of different parameters. Oryza sativa, Brachypodium distachyon, Solanum lycopersicum, Vitis vinifera, and Zea mays were also analyzed to demonstrate the broad applicability of this approach. Further, MGSE was also used to analyze Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans datasets to show its utility beyond plants. Mapping-based Genome Size Estimation (MGSE) and additional scripts are available on GitHub: https://github.com/bpucker/MGSE . MGSE predicts genome sizes based on short reads or long reads requiring a minimal coverage of 5-fold.

Chromosome-scale assembly of Artemia tibetiana genome, first aquatic invertebrate genome from Tibet Plateau

Genomic-level studies on the adaptive evolution of animals in the Qinghai-Tibet Plateau have been rapidly increasing. However, most studies are concentrated on vertebrates, and there are few reports on invertebrates. Here, we report the chromosome-level genome assembly for the brine shrimp Artemia tibetiana from Kyêbxang Co, a high-altitude (4620 m above sea level) salt lake on the plateau, based on the combination of Illumina, Nanopore long-reads and Hi-C sequencing data. The assembled genome is 1.69 Gb, and 94.83% of the assembled sequences are anchored to 21 pseudo-chromosomes. Approximately 75% of the genome was identified as repetitive sequences, which is higher than most crustaceans documented so far. A total of 17,988 protein-coding genes were identified, among them 14,388 were functionally annotated. This genomic resource provides the foundation for whole-genome level investigation on the genetic adaptation of Artemia to the harsh conditions in the Qinghai-Tibet Plateau.

Gap-free genome assembly and comparative analysis reveal the evolution and lignin degradation mechanisms of Cylindrobasidium torrendii

The Physalacriaceae family comprises numerous saprophytic edible and medicinal fungi with significant ecological and economic importance. However, the lack of high-quality genomic data has hindered systematic studies of this family. Here, we report the chromosome-level genome assembly of Cylindrobasidium torrendii, a species identified in China, using a combination of Illumina, PacBio HiFi, and Hi-C sequencing technologies. The 33.67 Mb genome, featuring a GC content of 52.00 %, demonstrates enhanced continuity and completeness. Phylogenetic analysis based on 1685 single-copy orthologous gene families places C. torrendii in close evolutionary proximity to Armillaria mellea and Gymnopus necrorhizus, with a divergence time of 112.39 Mya. Comparative genomics reveals conserved syntenic blocks between chromosomes of C. torrendii and those of Pleurotus ostreatus and Lentinula edodes. Gene family analysis identified 980 expanded and 487 contracted gene families, with expanded genes significantly enriched in secondary metabolite biosynthesis pathways. CAZyme, P450, and laccase gene family comparisons highlighted the evolutionary dynamics of these gene families in C. torrendii. Transcriptomic analysis under fungal dark stress revealed significant upregulation of genes such as CtoLAC7 and CAZymes (GH and CE families). This study provides a high-quality genomic resource and novel insights into the genetic and functional characteristics of C. torrendii and the Physalacriaceae family.

Low Heterozygosity and Historical Bottleneck Effect Depicted From the Genome Assembly of the Indus River Dolphin (Platanista minor)

The Indus River dolphin (Platanista minor) is a highly endangered freshwater dolphin endemic to the Indus River system of the Indian subcontinent. We reported a de novo assembly and characterization of the draft genome of the Indus River dolphin by using Illumina short-read sequencing technology. Based on this, for the first time, we conducted the comparative genomics study and identified a selection of genes and gene families that have undergone significant positive selection and expansion or contraction, indicating potential molecular mechanisms associated with freshwater adaptation, such as specialized skin features and their derivatives (e.g., hair loss) and immune adaptations. Additionally, this study estimated that the Indus River dolphin diverged nearly 31.2 million years ago from the most recent common ancestor of Delphinidae and Lipotidae, placing it in a more basal position to other freshwater dolphins (e.g., the baiji Lipotes vexillifer). It was suggested that the combined effects of the natural historical bottleneck effect around 40-20 kiloyears ago and anthropogenic activities were the driving factors of inbreeding for this species with very low heterozygosity (0.0218%).

Validation of male-specific markers confirmed an XY/XX-type sex determination system in Chinese dark sleeper (Odontobutis sinensis)

Next generation sequencing (NGS) method has been successfully used to identify sex-specific markers in many fish species. The Chinese dark sleeper (Odontobutis sinensis) is a commercially important aquaculture species in China. Here, by conducting whole genome sequencing of three females, three males and one female mixed pool, we initially identified 658 male-specific sequences and 242 female-specific sequences of Chinese dark sleeper. Based on polymerase chain reaction (PCR) confirmation, three markers showed 100 % male-specific amplification in 16 female and 16 male individuals from the Wuhan population, and this result was further validated using an additional 16 females and 16 males from the Guangdong population, demonstrating the reliability of these markers across multiple populations. These findings suggest a male heterogametic sex determination system in Chinese dark sleeper. Moreover, male-specific genes including high mobility group box 3 (hmgxb3) and insulin-like growth factor 2b (igf2b) were identified through NR annotation, which might be candidate sex-determining genes in Chinese dark sleeper. Generally, these validated male-specific markers first demonstrated the existence of an XY-type sex determination system in Chinese dark sleeper and would make a significant contribution to the development of all-male breeding and understanding of sex determination mechanisms.

In a nutshell: pistachio genome and kernel development

Pistachio is a sustainable nut crop with exceptional climate resilience and nutritional value. However, the molecular processes underlying pistachio nut development and nutritional traits are largely unknown, compounded by limited genomic and molecular resources. To advance pistachios as a future food source and a model system for hard-shelled fruits, we generated a chromosome-scale reference genome of the most widely grown pistachio cultivar (Pistacia vera 'Kerman') and a spatiotemporal study of nut development. We integrated tissue-level physiological data from thousands of nuts over three growing seasons with transcriptomic data encompassing 14 developmental time points of the hull, shell, and kernel to assemble gene modules associated with physiological changes. Our study defined four distinct stages of pistachio nut growth and maturation. We then focused on the kernel to identify transcriptional and metabolic changes in molecular pathways governing nutritional quality, such as the accumulation of unsaturated fatty acids, which are vital for shelf life and dietary value. These findings revealed key candidate conserved regulatory genes, such as PvAP2-WRI1 and PvNFYB-LEC1, likely involved in oil accumulation in kernels. This work yields new knowledge and resources that will inform other woody crops and facilitate further improvement of pistachio as a globally significant, sustainable, and nutritious crop.

The chromosome-level genome of Centella asiatica provides insights into triterpenoid biosynthesis

Centella asiatica is a well-known herbal plant that makes a significant contribution to the treatment of various chronic ailments. Triterpenoid saponins are the main active components extracted from C. asiatica, which have rich pharmacological activity. However, only a few studies have systematically elucidated the molecular mechanism underlying the biosynthesis of triterpenoid saponins in C. asiatica. Here, we report a chromosome-level reference genome of C. asiatica, by using Illumina, PacBio HiFi, and Hi-C technologies. The assembled genome exhibits high quality with a size of 455 Mb and a contig N50 of 36 Mb. A total of 26,479 protein-coding genes were predicted. Comparative genomic analysis revealed that the gene families involved in triterpenoid saponin biosynthesis, including squalene synthase (SS) and farnesyl diphosphate synthase (FPS), rapidly expanded in the C. asiatica genome. In particular, we have discovered two whole-genome duplication events in C. asiatica genomes. A further comprehensive analysis of the metabolome and transcriptome was performed using different tissues of C. asiatica in order to identify the key genes associated with triterpenoid saponin biosynthesis. Consequently, seven enzyme genes were considered to play important roles in triterpenoid biosynthesis. Subsequent functional characterization of CaOSC4 demonstrated that it is responsible for the biosynthesis of three ursane-type triterpenoids in C. asiatica. Our research establishes a genomic data platform that can be employed in the excavation of genes and precision breeding in C. asiatica. Additionally, the results offer new insights into the biosynthesis of triterpenoid saponins.

The First De Novo HiFi Genome Assemblies for Three Clownfish-hosting Sea Anemone Species (Anthozoa: Actiniaria)

The symbiosis between clownfish and giant tropical sea anemones (Order Actiniaria) is one of the most iconic on the planet. Distributed on tropical reefs, 28 species of clownfishes form obligate mutualistic relationships with 10 nominal species of venomous sea anemones. Our understanding of the symbiosis is limited by the fact that most research has been focused on the clownfishes. Chromosome-scale reference genomes are available for all clownfish species, yet only short reads-based reference genomes are available for five species of host sea anemones. Recent studies have shown that the clownfish-hosting sea anemones belong to three distinct clades of sea anemones that have evolved symbiosis with clownfishes independently. Here we present the first high-quality long-read assemblies for three species of clownfish-hosting sea anemones belonging to each of these clades: Entacmaea quadricolor, Stichodactyla haddoni, and Radianthus doreensis. PacBio HiFi sequencing yielded 1,597,562, 3,101,773, and 1,918,148 million reads for E. quadricolor, S. haddoni, and R. doreensis, respectively. All three assemblies were highly contiguous and complete with N50 values above 4 Mb and BUSCO completeness above 95% on the Metazoa dataset. Genome structural annotation with BRAKER3 predicted 20,454, 18,948, and 17,056 protein-coding genes in E. quadricolor, S. haddoni, and R. doreensis genome, respectively. These new resources will form the basis of comparative genomic analyses that will allow us to deepen our understanding of this mutualism from the host perspective.

Chromosome-Level Genome Assembly and Annotation of the Amur Rat Snake Elaphe schrenckii

The Amur rat snake (Elaphe schrenckii), a widely distributed colubrid species in Northeast Asia, plays a critical role in controlling rodent and mouse populations in the wild. Despite its ecological and evolutionary significance, genomic resources for this nonvenomous species have been limited. In this study, we present a high-quality, chromosome-level genome assembly of E. schrenckii, generated by PacBio HiFi long-read sequencing and Hi-C chromatin interaction mapping. The assembled genome size comprises 1.69 Gb, with a scaffold N50 length of 215 Mb. Hi-C scaffolding anchored the genome into 18 chromosomes, including one that represents the conserved Z chromosome of snakes, consistent with karyotypic observations. This assembly enables further gene annotation and analysis of chromosomal synteny patterns. Repetitive elements account for 53.2% of the genome, with long interspersed nuclear element retrotransposons being the predominant class (23.2%). We identified 18,529 protein-coding genes, with 90.6% functionally annotated through homology-based methods. The genome assembly is highly complete, with a BUSCO score of 97.4% (tetrapoda_odb10). This resource provides a foundation for comparative studies of colubrid genome evolution, which also serves as a crucial reference for conservation genomics, particularly for Asian snake populations facing habitat fragmentation.

Chromosome-level genome assembly of the sap beetle Glischrochilus (Librodor) japonius (Coleoptera: Nitidulidae)

Sap beetles are widely distributed in the Holarctic and tropical regions, with diverse feeding habits and strong adaptability. They play important roles in the decay of plants, the spread of fungi and bacteria, and the carbon and nitrogen cycles in agricultural ecosystems. Here, we provide an annotated, chromosome level reference genome assembly for a sap beetle Glischrochilus (Librodor) japonius (Motschulsky, 1857), a member of the family Nitidulidae, assembled using PacBio HiFi and Hi-C data from female specimens. The final assembly has a total size of 789.06 Mb, with 94.91% of the sequence successfully anchored to 10 chromosomes. The scaffold N50 is 77.84 Mb, and BUSCO (endopterygota_odb10 database) completeness is 97.20%. Repetitive elements comprise 54.67% of the genome (431.38 Mb). We identified 1,673 noncoding RNAs and predicted 22,526 protein-coding genes in the genome. This genome will serve as a valuable resource for advancing our understanding of the evolution and ecology of sap beetles, and will facilitate comparative studies of genome structure within the Nitidulidae family.

Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica

Furocoumarins (FCs), important natural compounds with biodefense roles and pharmacological activities, are notably abundant in medicinal plant Angelica dahurica. However, its accumulation patterns over development stages in FC-enriched tissue, biosynthetic pathways, and regulatory mechanisms in A. dahurica remain elusive. Here, we quantified the concentration dynamics of 17 coumarins across six developmental stages of root and found a gradual decrease in FC concentration as the roots develop. Using a de-novo assembled chromosome-level genome for A. dahurica, we conducted integrative multi-omics analyses to screen out candidate genes to fill in the sole missing step in the biosynthesis of imperatorin and isoimperatorin. This revealed that CYP71AZ18 catalyzes hydroxylation at the C-5 position of psoralen to generate bergaptol, while CYP71AZ19 and CYP83F95 catalyze hydroxylation at the C-8 position to produce xanthotoxol, notably indicating that a single step is catalyzed by two genes from distinct CYP450 subfamilies in this species. CYP71AZ19 originated from a proximal duplication event of CYP71AZ18, specific to A. dahurica, and subsequently underwent neofunctionalization. Accessible chromatin regions (ACRs), especially proximal ACRs, correlated with high gene expression levels, and the three validated genes exhibited strong signals of ACRs, showing the importance of chromosomal accessibility in regulating metabolite biosynthesis.

A chromosome-level genome assembly of Gray's grenadier anchovy, Coilia grayii

Gray's grenadier anchovy, Coilia grayii, is an important anadromous fish species with economic value in near ocean ecosystems. Despite its significance, the lack of genomic resources has constrained our understanding of its genetic foundation, phylogenetic relationships, and adaptive evolution strategies. In this study, we assembled a chromosome-level reference genome for C. grayii by integrating PacBio HiFi long-reads, MGI short-reads, and Hi-C sequencing data. The resulting genome is 920.64 Mb in size, with a contig N50 of 36.45 Mb. The genome contains 324.19 Mb of repetitive sequences, and 29,496 protein-coding genes were predicted, with 29,395 functionally annotated. BUSCO analysis revealed that 95.2% of the 3,640 benchmarking genes were complete, underscoring the high quality of the assembly. This high-quality genome will provide crucial insights into the phylogeny, evolutionary history, and genetic basis of adaptive traits in Coilia species.

De novo genome assembly of the Edwardsiid anthozoan Edwardsia elegans

Cnidarians (sea anemones, corals, hydroids, and jellyfish) are a key outgroup for comparisons with bilateral animals to trace the evolution of genomic complexity and diversity within the animal kingdom, as they separated from most other animals 100 s of million years ago. Cnidarians have extensive diversity, yet the paucity of genomic resources limits our ability to compare genomic variation between cnidarian clades and species. Here, we report the genome for Edwardsia elegans, a sea anemone in the most specious genus of the family Edwardsiidae, a phylogenetically important family of sea anemones that contains the model anemone Nematostella vectensis. The E. elegans genome is 396 Mb in length and is predicted to encode approximately 49,000 proteins. We annotated a large conservation of macrosynteny between E. elegans and other Edwardsiidae anemones as well as conservation of both microRNAs and ultra-conserved noncoding elements previously reported in other cnidarians species. We also highlight microsyntenic variation of clustered developmental genes and ancient gene clusters that vary between species of sea anemones, despite previous research showing conservation between cnidarians and bilaterians. Overall, our analysis of the E. elegans genome highlights the importance of using multiple species to represent a taxonomic group for genomic comparisons, where genomic variation can be missed for large and diverse clades.

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).

RAmbler resolves complex repeats in human Chromosomes 8, 19, and X

Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (2) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (3) uses the relative location of single-copy k-mers to barcode each HiFi read, (4) clusters HiFi reads based on their shared barcodes, (5) generates contigs by assembling the reads in each cluster, and (6) generates a consensus assembly from the overlap graph of the assembled contigs. Here, we show that RAmbler can reconstruct human centromeres and other complex repeats to a quality comparable to the manually curated Telomere-to-Telomere human genome assembly. Across more than 250 synthetic data sets, RAmbler outperforms hifiasm, LJA, HiCANU, and Verkko across various parameters such as repeat lengths, number of repeats, heterozygosity rates, and depth of sequencing.

Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity

Hawthorn (Crataegus pinnatifida) fruit peel color and seed hardness are key traits that significantly impact economic value. We present here the high-quality chromosome-scale genomes of two cultivars, including the hard-seed, yellow-peel C. pinnatifida "Jinruyi" (JRY) and the soft-seed, red-peel C. pinnatifida "Ruanzi" (RZ). The assembled genomes comprising 17 chromosomes are 809.1 Mb and 760.5 Mb in size, achieving scaffold N50 values of 48.5 Mb and 46.8 Mb for JRY and RZ, respectively. Comparative genomic analysis identifies 3.6-3.8 million single nucleotide polymorphisms, 8.5-9.3 million insertions/deletions, and approximately 30 Mb of presence/absence variations across different hawthorn genomes. Through integrating differentially expressed genes and accumulated metabolites, we filter candidate genes CpMYB114 and CpMYB44 associated with differences in hawthorn fruit peel color and seed hardness, respectively. Functional validation confirms that the CpMYB114-CpANS regulates anthocyanin biosynthesis in hawthorn peels, contributing to the observed variation in peel color. CpMYB44-CpCOMT is significantly upregulated in JRY and is verified to promote lignin biosynthesis, resulting in the distinction in seed hardness. Overall, this study reveals the new insights into understanding of distinct peel pigmentation and seed hardness in hawthorn and provides an abundant resource for molecular breeding.

The chromosome-scale genomes of two cultivated safflowers (Carthamus tinctorius) provide insights into the genetic diversity resulting from domestication

KEY MESSAGE

Two cultivated safflowers from distinct areas elucidate the genetic diversity present in the linoleic acid biosynthesis, flowering time and flavonoid biosynthesis. The process of domestication facilitates the adaptation of crops to agricultural environments. In this study, we selected two representative safflower cultivars that has been domesticated in two distinct areas in China as samples to investigate their genetic diversity due to local environmental adaption. Yunhong-7 is a locally bred safflower (Carthamus tinctorius) cultivar, that has been currently widely cultivated in Yunnan Province, Southwest China, and Anhui-1 is a safflower cultivar that was locally bred in Anhui Province, East China. We firstly generated the chromosome-scale genome assembly for yunhong-7 cultivar by combining PacBio and Hi-C technologies. Through comparative genomic analysis, we identified structural variations (SVs) between yunhong-7 and anhui-1, which revealed their genetic differences in the pathways of fatty acid biosynthesis, circadian rhythm and flavonoid biosynthesis. Subsequently, a total of 40 non-redundant fatty acid desaturase 2 (FAD2) genes (39 for yunhong-7 and 20 for anhui-1) were identified, revealing the presence of copy-number variation and major genes change between yunhong-7 and anhui-1. The presented results suggested that changes in SVs may induce alterations in the expression of flowering-related genes, which could explain the observed early flowering phenotype in yunhong-7 compared to anhui-1. We identified a total of 197 non-redundant UDP-glucuronosyltransferases (UGT) genes. Based on prokaryotic expression system, we investigated the catalytic functions of two unique UGT genes (CtUGT.18 and CtUGT.191). The current study increases our knowledge of genetic diversity among crop cultivars resulting from distinct domestication processes and thus could contribute to the advancement of traits research and the safflower breeding.

Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon

Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.

Diploid chromosome-level genome assembly and annotation for Lycorma delicatula

The spotted lanternfly (Lycorma delicatula) is a planthopper species (Hemiptera: Fulgoridae) native to China but invasive in South Korea, Japan, and the United States where it is a significant threat to agriculture. Genomic resources are critical to both management of this species and understanding the genomic characteristics of successful invaders. We report an annotated, haplotype-phased, chromosome-level genome assembly for the spotted lanternfly using PacBio long-read sequencing, Hi-C technology, and RNA-seq. The 2.2 Gbp genome comprises 13 chromosomes, and whole genome resequencing of eighty-two adults indicated chromosome four as the sex chromosome and a corresponding XO sex-determination system. We identified over 12,000 protein-coding genes and performed functional annotation, facilitating the identification of candidate genes that may hold importance for spotted lanternfly control. The assemblies and annotations were highly complete with over 96% of BUSCO genes complete regardless of the database (i.e., Eukaryota, Arthropoda, Insecta). This reference-quality genome will serve as an important resource for development and optimization of management practices for the spotted lanternfly and invasive species genomics as a whole.

Chromosome-level genome assembly of the traditional medicinal plant Lindera aggregata

Lindera aggregata is a renowned medicinal plant in China, particularly the variety from Tiantai, Zhejiang Province, which is esteemed for its superior medicinal properties. Beyond its medicinal value, it holds significant economic potential and phylogenetic significance. Utilizing a range of sequencing techniques, we have successfully assembled and annotated a high-quality chromosome-level genome of L. aggregata. The assembled genome spans approximately 1.59 Gb, with a scaffold N50 length of 132.62 Mb. Approximately 93.07% of the assembled sequences have been anchored to 12 pseudo-chromosomes, and 70.02% of the genome consists of repetitive sequences. According to the annotations, a total of 33,283 genes are identified, of which 96.95% can predict function. This high-quality chromosome-level assembly and annotation will greatly assist in the development and utilization of L. aggregata's valuable resources, and also provide a crucial molecular foundation for investigating the evolutionary relationships within the Lauraceae family and the mechanisms behind the synthesis of active ingredients in L. aggregata.

A-to-I RNA editing of CYP18A1 mediates transgenerational wing dimorphism in aphids

Wing dimorphism is a common phenomenon that plays key roles in the environmental adaptation of aphid; however, the signal transduction in response to environmental cues and the regulation mechanism related to this event remain unknown. Adenosine (A) to inosine (I) RNA editing is a post-transcriptional modification that extends transcriptome variety without altering the genome, playing essential roles in numerous biological and physiological processes. Here, we present a chromosome-level genome assembly of the rose-grain aphid Metopolophium dirhodum by using PacBio long HiFi reads and Hi-C technology. The final genome assembly for M. dirhodum is 447.8 Mb, with 98.50% of the assembled sequences anchored to nine chromosomes. The contig and scaffold N50 values are 7.82 and 37.54 Mb, respectively. A total of 18,003 protein-coding genes were predicted, of which 92.05% were functionally annotated. In addition, 11,678 A-to-I RNA-editing sites were systematically identified based on this assembled M. dirhodum genome, and two synonymous A-to-I RNA-editing sites on CYP18A1 were closely associated with transgenerational wing dimorphism induced by crowding. One of these A-to-I RNA-editing sites may prevent the binding of miR-3036-5p to CYP18A1, thus elevating CYP18A1 expression, decreasing 20E titer, and finally regulating the wing dimorphism of offspring. Meanwhile, crowding can also inhibit miR-3036-5p expression and further increase CYP18A1 abundance, resulting in winged offspring. These findings support that A-to-I RNA editing is a dynamic mechanism in the regulation of transgenerational wing dimorphism in aphids and would advance our understanding of the roles of RNA editing in environmental adaptability and phenotypic plasticity.

Comparative genomic and phylogenetic analysis of mitochondrial genomes of the Pseudo-nitzschia HAB species

The genus Pseudo-nitzschia within Bacillariophyta (diatoms) is best known for its rich collection of toxigenic harmful algal bloom (HAB) species capable of producing the neurotoxin domoic acid (DA), which causes amnesic shellfish poisoning (ASP) in humans. Molecular markers such as 18S rDNA, ITS1, and ITS2 have been applied to facilitate Pseudo-nitzschia species identification because morphology-based methods often could not adequately distinguish different species due to their morphological similarities and plasticity. In this study, we constructed mitochondrial genomes (mtDNAs) for 11 Pseudo-nitzschia species and assessed their utility as "super-barcodes" for species identification and evolutionary analysis. These mtDNAs exhibited conserved genome structures despite variability in repeat regions. A potential tatA-tatC gene fusion event was observed in a single Pseudo-nitzschia species P. brasiliana. We also observed intron variability in cox1 genes. Phylogenetic analyses of mtDNAs, chloroplast genomes (cpDNAs), and nuclear ribosomal DNA (nrDNA) arrays revealed consistent results, supporting the closely related but distinct clustering of the genera Fragilariopsis and Pseudo-nitzschia. We further designed a high-resolution molecular marker tatA for species identification based on the comparative analysis of these mtDNAs, which could be used to track Pseudo-nitzschia diversity. These findings offer new genome resources and new insights into the genetic evolution and classification of Pseudo-nitzschia, underscoring the need for continued research in this field.

Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization

A major goal of evolutionary biology is to identify the genetic basis for the emergence of complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in the genus Nitzschia, loss of photosynthesis led to a group of free-living secondary heterotrophs whose manner of acquiring chemical energy is unclear. Here, we sequence the genome of the non-photosynthetic diatom Nitzschia sing1 and identify the genetic basis for its catabolism of the brown algal cell wall polysaccharide alginate. N. sing1 obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from a marine bacterium. Subsequent gene duplication through unequal crossing over and transposition led to 91 genes in three distinct gene families. One family retains the ancestral endolytic enzyme function. By contrast, the two others underwent domain duplication, gain, loss, rearrangement, and mutation to encode novel functions that can account for oligosaccharide import through the endomembrane system and the exolytic production of alginate monosaccharides. Together, our results show how a single HGT event followed by substantial gene duplication and neofunctionalization led to alginate catabolism and access to a new ecological niche.

Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa

Populus trichocarpa, a pivotal model organism for woody transgenic research, not only garners substantial scientific interest but plays an integral role in forestry economics. Previous genomic assemblies of P. trichocarpa predominantly treated its heterozygous genome as homozygous, thereby neglecting crucial haplotypic diversity. Leveraging the high-fidelity (HiFi) sequencing capabilities of PacBio sequencing and the chromosome conformation capture insights provided by Illumina's Hi-C technique, this study is the first to achieve a near telomere-to-telomere assembly of both paternal and maternal haplotypes in P. trichocarpa. Comparative genomic analysis between these haplotypes has uncovered several allelic variants and pathways critical for trait determination through allele-specific expression. Furthermore, utilizing RNA-seq data from multiple tissues, this investigation has detailed the tissue-specific expression patterns of the leucine-rich repeat gene family, which are essential in mediating plant signal transduction and developmental regulation. Our results not only illuminate the functional genomics landscape of P. trichocarpa but also provide invaluable theoretical underpinnings for the genetic improvement of woody plants and a robust framework for exploring genetic variability and allelic expression disparities in arboreal species.

Origin and stepwise evolution of vertebrate lungs

Lungs are essential respiratory organs in terrestrial vertebrates, present in most bony fishes but absent in cartilaginous fishes, making them an ideal model for studying organ evolution. Here we analysed single-cell RNA sequencing data from adult and developing lungs across vertebrate species, revealing significant similarities in cell composition, developmental trajectories and gene expression patterns. Surprisingly, a large proportion of lung-related genes, coexpression patterns and many lung enhancers are present in cartilaginous fishes despite their lack of lungs, suggesting that a substantial genetic foundation for lung development existed in the last common ancestor of jawed vertebrates. In addition, the 1,040 enhancers that emerged since the last common ancestor of bony fishes probably contain lung-specific elements that led to the development of lungs. We further identified alveolar type 1 cells as a mammal-specific alveolar cell type, along with several mammal-specific genes, including ager and sfta2, that are highly expressed in lungs. Functional validation showed that deletion of sfta2 in mice leads to severe respiratory defects, highlighting its critical role in mammalian lung features. Our study provides comprehensive insights into the evolution of vertebrate lungs, demonstrating how both regulatory network modifications and the emergence of new genes have shaped lung development and specialization across species.

Chromosomal-Level Genome Suggests Adaptive Constraints Leading to the Historical Population Decline in an Extremely Endangered Plant

Increased human activity and climate change have significantly impacted wild habitats and increased the number of endangered species. Exploring evolutionary history and predicting adaptive potential using genomic data will facilitate species conservation and biodiversity recovery. Here, we examined the genome evolution of a critically endangered tree Pellacalyx yunnanensis, a plant species with extremely small populations (PSESP) that is narrowly distributed in Xishuangbanna, China. The species has neared extinction due to economic exploitation in recent decades. We assembled a chromosome-level genome of 334 Mb, with the N50 length of 20.5 Mb. Using the genome, we discovered that P. yunnanensis has undergone several population size reductions, leading to excess deleterious mutations. The species may possess low adaptive potential due to reduced genetic diversity and the loss of stress-responsive genes. We estimate that P. yunnanensis is the basal species of its genus and diverged from its relatives during global cooling, suggesting it was stranded in unsuitable environments during periods of dramatic climate change. In particular, the loss of seed dormancy leads to germination under unfavourable conditions and reproduction challenges. This dormancy loss may have occurred through genetic changes that suppress ABA signalling and the loss of genes involved in seed maturation. The high-quality genome has also enabled us to reveal phenotypic trait evolution in Rhizophoraceae and identify divergent adaptation to intertidal and inland habitats. In summary, our study elucidates mechanisms underlying the decline and evaluates the adaptive potential of P. yunnanensis to future climate change, informing future conservation efforts.

Chromosome-level genome assembly of the Adonis ladybird Hippodamia variegata

The Adonis ladybird (Hippodamia variegata), an important predator in agricultural ecosystems, plays a crucial role in biological control and is a significant model for evolutionary and genomic studies within Coccinellidae. Despite its ecological importance, the lack of a reference genome for H. variegata has limited in-depth investigations into its biology and potential as a biocontrol agent. Here, we present a high-quality, chromosome-level genome assembly of H. variegata. The final assembly spans 493.01 Mb, with a scaffold N50 of 28.19 Mb and a GC content of 36.41%. Hi-C sequencing data enabled the anchoring of 343.20 Mb to 10 chromosomes. Repetitive elements accounted for 258.56 Mb (52.44%) of the genome, with long interspersed nuclear elements (LINEs) being the most prevalent. We identified 37,348 protein-coding genes, of which 78.55% were functionally annotated in public protein databases. This high-quality genome assembly will serve as a valuable resource for furthering our understanding of Adonis ladybird's evolutionary biology, enhancing its utility in pest management, and supporting future research on ladybird genomics.

A high-quality chromosome-level genome assembly for the agricultural pest Mythimna separata

The oriental armyworm, Mythimna separata, poses a persistent challenge to agricultural pest management due to its strong migratory abilities and polyphagous feeding behavior. In this study, we present a chromosome-level genome assembly using Illumina, PacBio HiFi, and Hi-C sequencing technologies. The final assembly spans 714.5 Mb with a scaffold N50 of 22.7 Mb and a GC content of 38.8%. A total of 32 chromosomes were successfully anchored, including the Z and W sex chromosomes. BUSCO analysis indicated a genome completeness of 98.6%, and 19,879 protein-coding genes were predicted. The W chromosome, measuring 30.55 Mb with a repeat content of 68.34%, harbors 824 protein-coding genes. Furthermore, a PCR-based method confirmed W-linked sequences for female-specific sex detection via the ZW system. This enhanced genome assembly provides a valuable resource for evolutionary research on M. separata and facilitates the development of sex-regulated pest control strategies.

A taxonomic revision of the genus Raorchestes in Myanmar and Thailand with the description of two new species from Myanmar (Amphibia, Anura, Rhacophoridae)

We revise the frogs of the genus Raorchestes from Myanmar and Thailand based on data of external morphology, bioacoustics, and molecular genetics. The results of this integrative study provide evidence for the recognition of seven species, two of which we describe as new: Raorchestes mindat sp. nov. from Mindat District, Chin State, western Myanmar, and Raorchestes leiktho sp. nov. from Hpa-an District, Kayin State, southeastern Myanmar. The other species that we recognize in Myanmar and Thailand are R. cangyuanensis, R. huanglianshan, R. longchuanensis, R. menglaensis, and R. parvulus. We have compared the external morphology of the lectotype and four paralectotypes of Ixalus parvulus Boulenger, 1893 with the species of the Raorchestes parvulus group currently recognized from South-east Asia. Although the type series of Ixalus parvulus is morphologically most similar to specimens of R. cangyuanensis from Thailand, we refrain from formally synonymizing these two taxa until genetic data for I. parvulus are available that would allow this hypothesis to be tested. Thus, R. parvulus remains an enigmatic taxon still only known from the original type series. As now defined, R. cangyuanensis is distributed across most of Myanmar except for the Malayan Peninsula, and also in adjacent Yunnan Province, China, and adjacent northeastern Bangladesh. Raorchestes longchuanensis occurs in northwestern Thailand as well as in eastern Myanmar and western Yunnan, China. Raorchestes menglaensis ranges from southern Yunnan, China, across Thailand, Laos, and Cambodia to northern Western Malaysia. Raorchestes huanglianshan is distributed in southern Yunnan, China, and northwestern Thailand. Often two, at some places even three species of this genus occur sympatrically (e.g., R. leiktho sp. nov., R. longchuanensis and R. parvulus near Leiktho, Kayin State, Myanmar; R. longchuanensis and R. huanglianshan at Doi Inthanon). We provide new bioacoustic data for R. longchuanensis, R. menglaensis, and R. leiktho sp. nov., and compare these with data of R. cangyuanensis and R. rezakhani.

Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Crucian carp (Carassius carassius), a member of the carp family (Cyprinidae), is known for its remarkable anoxia tolerance. The physiological responses and adaptations to anoxia are well documented, but there is a need for better understanding of the molecular regulation and evolutionary mechanisms behind these adaptations. Here we present a high-quality, functionally annotated, chromosome-level genome assembly that can facilitate such further studies. Genomic DNA was obtained from a wild-caught crucian carp specimen and used for PacBio long-read, Illumina short-read and Hi-C sequencing. Short-read mRNA data were used for structural annotation using the BRAKER3 pipeline, while PacBio long-read RNA sequencing data were used for annotation of untranslated regions and refinement of gene-isoform relationships, using the PASA pipeline. The full assembly had a contig-level N50 of 15Mbp in 290 scaffolds and 98.6% of the total length (1.65Gbp) placed in 50 chromosomes. Structural annotation resulted in 82,557 protein-coding transcripts (in 45,667 genes), with a BUSCO completeness of 99.6% and of which 77,370 matched a protein in the UniProtKB/Swiss-Prot database.

Comparative genomics provides insights into the biogeographic and biochemical diversity of meliaceous species

Meliaceous plants such as Azadirachta indica (neem) and Melia azedarach (chinaberry) contain large amounts of limonoids with unique anti-insect activities. However, genes responsible for downstream modifications of limonoids are not well known. Here, we improve the genome assemblies of neem and chinaberry to the telomere-to-telomere (T2T) level. Allopatric speciation of the two plants is confirmed by the lineage-specific inversion of chromosome 12 in the neem lineage. We further identify two BAHD-acetyltransferases (ATs) in chinaberry (MaAT8824 and MaAT1704) that catalyse acetylation at both the C-12 and C-3 hydroxyl groups of limonoids, whereas the syntenic neem copy (AiAT0635) does not possess this activity. A critical N-terminal region (SAGAVP) is crucial for the acetylation of AiAT0635, and swapping it into the MaAT8824 version (CHRSSG) can endow it with acetylation activity. Our improved genome assemblies provide insights into allopatric speciation of neem, as well as limonoid biosynthesis and chemical diversity in meliaceous plants.

Insights into dill (Anethum graveolens) flavor formation via integrative analysis of chromosomal-scale genome, metabolome and transcriptome

INTRODUCTION

Dill (Anethum graveolens) is a significant medicinal herb belonging to the Apiaceae family. Owing to its high levels of volatile organic compounds (VOCs), dill is commonly utilized for essential oil extraction and medicine purpose. However, the biosynthesis of the crucial VOC in dill remains obscure.

OBJECTIVES

Identify the key VOCs related to the flavor formation in dill and dissect the regulatory mechanism of their synthesis.

METHODS

The dill chromosomal-level genome was constructed by PacBio HiFi, Hi-C, and BGISEQ second generation sequencing and assembly. The VOCs in dill leaves were identified through GC-MS. The potential mechanism involved in regulating the VOC accumulation in dill flavor formation was analyzed by multi-omics analysis.

RESULTS

A 1.17 Gb chromosome-scale genome of dill with a contig N50 of 10.78 Mb was constructed. A total of 46,538 genes were annotated across 11 assembled chromosomes. Comparative genomics analysis suggested that transposable element insertions, especially LTR-Gypsy, have contributed to the evolution and expansion of the dill genome. The flavor formation of dill was mainly attributed to terpenoids, especially α-phellandrene, β-ocimene, and o-cymene. The contribution of expansion and replication of terpenoid synthesis pathway genes, especially terpene synthase (TPS), to the abundant terpenoid production of dill was identified. Differential gene expression patterns observed at various developmental stages and tissues provided key candidate genes for the regulation of terpenoid synthesis, as well as transcription factors. The different accumulation of esters and aromatics also affected the flavor formation of dill. The key genes implicated in the synthesis of anethole, namely AIS and AMT were further identified.

CONCLUSION

This study constructed the chromosome level genome and identified the main VOCs and related key genes in flavor formation of dill, shedding lights on our understanding of terpenoid biosynthesis but also offered guidance for future genetic research on molecular breeding in Anethum graveolens.

Chromosome-level genome assembly of a critically endangered species Leuciscus chuanchicus

Leuciscus chuanchicus, a critically endangered cyprinid endemic in the Yellow River, represents an evolutionary significant lineage within Leuciscinae. However, conservation efforts for this species have been hindered by the lack of genetic and genomic resources. Here we reported a high-quality chromosome-level genome of L. chuanchicus by combining Illumina reads, PacBio HiFi long reads and Hi-C data. The assembled genome size was 1.16 Gb, with a contig N50 size of 31,116,631 bp and a scaffold N50 size of 43,855,677 bp. The resulting 130 scaffolds were further clustered and ordered into 25 chromosomes based on the Hi-C data, representing 97.84% of the assembled sequences. The genome contained 60.36% repetitive sequences and 35,014 noncoding RNAs. A total of 31,196 protein-coding genes were predicted, of which 28,323 (90.79%) were functionally annotated. The BUSCO and OMArk revealed 97.6% and 91.28% completion rates, respectively. This study assembled a high-quality genome of L. chuanchicus, and provided fundamental genomic resources for investigating the molecular mechanism and evolution of the Leuciscinae.