Rapidly evolving begomoviruses are a serious threat to cash crops worldwide. Perennial plants often harbor these viruses for a long time, making them accessible to crop plants. Perennial ornamental plants Duranta erecta variegata (Variegated Sky Flower) were found with typical begomoviral symptoms, including leaf curling, leaf deformation, and leaf shortening in the plant nurseries of Faisalabad, Pakistan, in 2021. Begomovirus and its associated satellite molecules of 2.8 and 1.4 kb, respectively, were amplified using rolling circle amplification (RCA). Sanger sequencing of cloned molecules revealed the presence of rose leaf curl virus (RoLCuV, Begomovirus rosae) accompanied by a novel recombinant DNA-B, tentatively named “rose leaf curl virus DNA-B,” along with hollyhock yellow vein alphasatellite (HYVA, Gosmusatellite alceae). Another plant sample showed the presence of agriculturally important papaya leaf crumple virus (PaLCrV, Begomovirus papayae). To our knowledge, this is the first report of RoLCuV, a novel DNA-B, PaLCrV, and HYVA infecting D. erecta variegata in Pakistan.

Kousa dogwood (Cornus kousa Hance) is a popular flowering ornamental tree in the United States (U.S.), largely due to its pest and disease tolerance. Here, we present the first chromosome-scale, diploid genome assembly of C. kousa K2, a foundational breeding parent. The final chromosome-scale genome assemblies are 1602.739 Mb for Hap 1 and 1598.929 Mb for Hap 2. The complete Benchmarking Universal Single-Copy Ortholog (BUSCO) for Hap 1 and 2 were 98.8% and 98.4%, respectively. Between the two haplotypes, 98.97% of the genome is placed into chromosomes. 30,799 and 31,044 genes were annotated in Hap 1 and Hap 2, respectively. This annotated genome assembly for C. kousa provides insight into the genomic composition of the species and will enhance our understanding of the genetic control of traits of interest in breeding programs and the evolutionary history of the Cornus genus.

Common garden experiments have provided great insights into crop adaptation across many systems. Cotton (Gossypium spp.) cultivars have changed in the 20th and 21st centuries, but breeders have not quantified the degree of these changes. We synthesized a panel of 164 non-genetically modified genotypes, from the private and public sectors, which we refer to as the "US Historical Lines Panel." We collected historical documentation, including parentage and time of release, to group each genotype into one of four eras. We grew all genotypes in a common garden experiment, collected data, and then used univariate and bivariate statistical methods to analyze the changes in cotton trait genetic architecture over time. Through this comprehensive analysis we found that cotton breeders have improved average cotton fiber quality and yield. The variance for traits and their pairwise correlations have also undergone significant changes. We estimated that the net genetic gain accounts for 46% of the increase in historical fiber yield increase. Our results lay the groundwork for future analysis on the cotton historical lines, providing a long-term historical and phenotypic resource for follow-up experiments.

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass species in the family Poaceae. This species is a popular choice for lawns in the Southern United States, due to its higher tolerance to shade, heat and humidity. However, there is little genomic information available to researchers and breeders, limiting knowledge on the genetic basis for favorable traits. We present a reference-grade chromosome-scale genome assembly for the popular freeze-tolerant diploid cultivar Raleigh. The reference genome has been resolved into two haplotype assemblies (465.41 and 401.52 Mb), accounting for 95.2% and 82.1% of the expected haplotype genome size respectively, each anchored on the nine chromosomes and a total of 62,454 genes. Analysis of the assembly revealed 50.70% of the genome contained repeats. Analysis of the diversity within the species was investigated across 79 genotypes including commercial cultivars, breeding lines, and plant introductions by low-coverage sequencing identifying 605,038 single nucleotide polymorphisms (SNPs). The SNPs were used to investigate genetic diversity across the panel and the effectiveness of low-coverage sequencing on the high GC content species. SNPs classified genotypes into groups matching their phylogenetic and breeding history, with the plant introductions clustering into two groups on either side of the plot. Breeding lines for those whose parents existed in the panel clustered in between the two parents. These results showed that the cheaper, low-coverage option can be used for this type of analysis. Together, all of the resources produced in this study allow the start of the genomics-enabled genetic improvement for St. Augustinegrass.

Rainbow trout (Oncorhynchus mykiss) exhibit extensive genomic diversity shaped by domestication, life history and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemblies of two genetically and ecologically distinct lines: Whale Rock (WR; wild, landlocked, Central California) and Keithley Creek (KC; wild, resident, interior Columbia Basin), along with the previously published assemblies of the Arlee (domesticated, Northern California) and Swanson (semi-domesticated, resident, Alaska) lines. All assemblies provide nearly complete coverage of known genes (BUSCO 95.8%-99.7%) and are similar in genome size (~2.3 Gb), with scaffold N50 values between 3.4 Mb (KC) and 52.4 Mb (Swanson). Comparative whole-genome alignments revealed high sequence conservation (97%-98% identity) among assemblies, but also evidence of extensive structural variation of at least 50 bp in length. Structural variant (SV) profiling identified tens of thousands of deletions, insertions and complex rearrangements largely in noncoding sequences. In an initial assessment of the utility of having multiple de novo genome assemblies for rainbow trout, we found that two strains (Arlee and Swanson; domesticated) share SVs enriched in genes linked with growth, reproduction and adaptation to domestication, such as GTP binding and ECM-receptor interaction. In comparison, the other two strains (WR and KC; wild origin) share SVs associated with reproductive timing, such as the GnRH signalling pathway. Both Arlee and WR also have unique SVs potentially related to their geographic origin and unique life history. Additionally, we identified SVs in key regions, such as a QTL for fillet yield on Omy17 and the maturation-associated six6/erβ-gphb5 locus on Omy25q, suggesting the importance of considering SVs when investigating the genomics of complex traits. Together, these assemblies and comparative analyses establish a foundation for a rainbow trout pangenome reference, illuminating how they can be utilized to reveal the structural genomic basis of domestication, adaptation, and other complex traits in O. mykiss.

The genome of the Swanson doubled haploid (DH) YY male line of rainbow trout was de novo assembled using the Canu pipeline, high-coverage PacBio long-read sequence data, Bionano optical maps, and Hi-C proximity ligation sequence data, resulting in 29 major scaffolds aligning with the karyotype of the Swanson line (2 N = 58). This assembly, totaling 2.3 Gb with an N50 of 52.4 Mb, represents approximately 95% of the genome in 29 chromosome sequences with only 109 gaps between scaffolds. Notably, corrections to previous errors in the Swanson line genome assembly were made, including the identification of a double large inversion on the Omy05 chromosome (~57 Mb), the absence of the Omy20 inversion between the Arlee and Swanson assemblies, and the discovery of a ~6.7 Mb inversion on Omy26. This comprehensive assembly contributes to refining the rainbow trout reference genome and serves as a valuable resource for future genetic studies within this species.

A total of 768 molecular markers were developed for Ipomoea batatas (L.) Lam., consisting of 689 simple sequence repeats (SSRs) and 79 single nucleotide polymorphisms (SNPs). All the markers were distributed across the sweet potato genome, averaging 51 markers per chromosome. The markers were tested on DNA samples from five cultivars of I. batatas, assessing their amplification efficiency and polymorphism. Here we provide the primer sequences tested, their chromosome locations, the analysis including amplicon sizes, and highlight 92 that showed polymorphism between Beauregard and Tanzania. This dataset offers valuable resources for constructing high-resolution linkage maps and facilitates advanced genetic studies and breeding programs in sweetpotato.

Cotton Leaf Curl Disease (CLCuD) has been causing substantial yield losses to the cotton crop in South Asia since its first epidemic in the early 1990s. Researchers face several problems while screening and breeding for CLCuD-resistant varieties due to absence of a reliable screening system, controversial inheritance data, limited genetic information about resistance sources, rapid evolution of viral strains, recombination between two virus groups, narrow plant genetic base, poor management practices, and reliance on small segregating populations. These factors have led to the failure of several cotton varieties that were initially released as resistant to Cotton Leaf Curl Virus (CLCuV). Hence, in the present study, a highly CLCuV-susceptible breeding line, Stoneville-47, tagged with a herbicide resistance marker gene (Round-Up-ready cotton), was crossed with newly discovered resistant accessions, Mac-07 and USG13_1087, to gain insights into the genetic inheritance patterns of resistance against CLCuD. Screening of breeding material against CLCuD resulted in thirty-each resistant (S-0), and susceptible plants (S1-S4) upon grafting with susceptible scions. The qPCR further validated the results, as no viral or betasatellite DNA was detected in resistant plants, unlike the susceptible ones. The Chi-square test of F1 and F2 generations revealed the presence of a single dominant gene or closely linked QTLs with involvement of certain modifying factors or suppressors, controlling CLCuD resistance. These findings suggest that backcross breeding is a suitable method to introduce disease resistance. The circumvention of the suppressors of resistance from the selected progenies can be achieved by raising larger plant populations. However, there is still a need to fine-map the resistance loci, identify key haplotypes, and validate them across diverse genetic backgrounds. Moreover, pyramiding these clusters maybe a straightforward approach to advancing the development of CLCuD-resistant cotton varieties.

Deformed wing virus (DWV) can cause a major disease in honeybees worldwide and has been detected in many other arthropods (S. J. Martin and L. E. Brettell, Annu Rev Virol 6:49-69, 2019, https://www.annualreviews.org/content/journals/10.1146/annurev-virology-092818-015700). The presence and replication of DWV in Solenopsis invicta (red fire ant) were confirmed (G. P. Miles, X. F. Liu, E. Amiri, M. J. Grodowitz, et al., Insects 14:788, 2023, https://www.mdpi.com/2075-4450/14/10/788). Here, we document the DWV-A near-complete genome sequence from S. invicta in Mississippi, USA.

Fine mapping of the leaf rust susceptibility gene Sph1 identified a receptor-like kinase-encoding gene as a candidate and provided user-friendly markers for barley breeding. Caused by the biotrophic fungal pathogen Puccinia hordei, leaf rust is one of the important foliar diseases in barley. Although a few dominant genes for leaf rust resistance have been identified and cloned in barley, resistance conferred by major genes has been frequently defeated by the pathogen. A recessive resistance was identified in a spring barley accession using the P. hordei isolate VA90-34 which is virulent to most of major resistance genes. To localize this recessive resistance (hereafter named Susceptibility to P. hordei 1 or Sph1 indicating that the dominant allele confers disease susceptibility), we conducted fine mapping with an F2 population and molecular markers in the present study. The Sph1 gene was anchored near the telomere of the short arm of chromosome 3H, delimited within an ⁓560 kb region in the dominant parent. Of the six predicted genes in the Sph1 region, a gene encoding putative receptor-like kinase was selected as a candidate for functional validation. Therefore, our study provides a high-resolution genetic map and candidate for Sph1, building a foundation for the cloning of this important gene.

Mango ( Mangifera spp.) is a major tropical fruit crop of global economic importance, but advanced genomic resources are needed to support its breeding, conservation, and sustainable cultivation. In this study, a mango pangenome was constructed using high-quality, telomere-to-telomere genomes of four cultivated mango ( M. indica ) accessions representing distinct genetic origins, and one wild relative, M. odorata . Genome-wide analyses revealed a significant reduction in heterozygosity among elite commercial cultivars, indicating a genetic bottleneck resulting from long-term artificial selection. Core genes were enriched in fundamental biological pathways, including primary metabolism, photosynthesis, transcriptional regulation, and cellular signaling. Variable genes were primarily associated with secondary metabolite biosynthesis, reflecting local environmental adaptations. Pangenome and comparative genomic analyses identified structural variations among accessions. Additionally, 10,482 high-confidence single nucleotide polymorphisms (SNPs) were detected and utilized for population genomic analysis of 197 mango accessions, delineating four genetically distinct groups. Southeast Asian accessions exhibited unique genetic diversity and divergence from Caribbean, Indian, and U.S. groups. Comparative analyses revealed differentiation in specialized metabolic pathways, particularly alkaloid and diterpenoid biosynthesis, likely reflecting adaptive responses to the complex ecological interactions and high biodiversity of Southeast Asian tropical rainforests. Genomic analysis of the MiRWP gene, associated with apomixis, provided comprehensive insights into this important mango trait, demonstrating the potential of the pangenome for future mango breeding efforts. The genomic resources generated in this study establish a critical foundation for advancing mango genetic research, facilitating trait improvement, and informing conservation strategies. ### Competing Interest Statement The authors have declared no competing interest. This work was supported by the United States Department of Agriculture - Agricultural Research Service CRIS Project Number 6066-21310-006-00D and grant number 58-6066-9-006.

The North American-native ornamental tree, flowering dogwood (Cornus florida L.), has a showy bract display that can range in color from white to pink to deep red. Although many trees have white bracts, there is consumer demand for novel pigmentation in the bracts combined with other traits of interest. Because the genetic basis of all traits in flowering dogwood is unknown, combining them using traditional breeding efforts is time, labor, and space-intensive. We developed foundational genomic resources to establish marker-assisted selection within flowering dogwood breeding. We generated diploid, chromosome-scale, annotated genome assemblies for one pink-bracted and red-leafed tree and one white-bracted and green-leafed tree. Additionally, a phenotyping protocol for bract color and presence/absence diagnostic SNPs for bract and leaf color were established. We leveraged these resources to evaluate linkage associations and differential gene expression related to anthocyanin biosynthesis to identify candidate genes regulating bract and leaf pigmentation. Within a 14 Mb locus we identified 14 anthocyanin-related genes. Two genes, with MYB (g19533) and RING finger (g19556) binding domains, had both differential gene expression and variants with the expected segregation pattern. These candidate genes, diagnostic SNPs, and genomic resources will be valuable in combining pink-red bracts with other traits to advance flowering dogwood breeding.

Sugar beet (Beta vulgaris L.) is a global source of table sugar and animal fodder. Here we report a highly contiguous, haplotype phased genome assembly and annotation for sugar beet line FC309. Both assembled haplomes for FC309 represent the largest and most contiguous assembled beet genomes reported to date, as well as gene annotations sets that capture over 1,500 additional protein-coding loci compared to prior beet genome annotations. These new genomic resources were used to identify novel quantitative trait loci (QTL) for Fusarium yellows resistance from the FC309 genetic background using an F2 mapping-by-sequencing approach. The highest QTL signals were detected on Chromosome 3, spanning approximately 10Mbp in both haplomes. A parallel transcriptome profiling experiment identified candidate genes within the Chromosome 3 QTL with plausible roles in disease response, including NBS-LRR genes with expression trends supporting a role in resistance. Investigation of genetic variants in these candidate genes found 1 major disease-resistance protein containing high-effect variants of interest. Collectively, the genomic resources for FC309 presented here are foundational tools for comparative genomics, mapping other traits in the FC309 background, and as a reference genome for other beet studies due to its contiguity, completeness, and high-quality gene annotations.

Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (Oncorhynchus mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests that they may represent distinct species. In this study, we produced a chromosomal-level genome assembly and a genetic map for one of the species in the cutthroat trout species complex, the westslope cutthroat trout (Oncorhynchus lewisi-formerly Oncorhynchus clarkii lewisi). We also constructed haplotype-resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. We used the new genome assemblies to identify major interspecific chromosomal rearrangements between the 2 sister species, including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights regarding genetic variation within cutthroat trout and in hybrids between rainbow and cutthroat trout.

The soft tick family Argasidae contains vectors of medical and veterinary importance, but few molecular resources are available compared to hard ticks (Ixodidae). One example is Ornithodoros turicata, a recognized vector of Borrelia turicatae, causal agent of human relapsing fever, and a putative vector of African swine fever virus. To address the current lack of molecular resources for the Argasidae, we generated a chromosome-level genome assembly for O. turicata using PacBio sequencing in conjunction with an Illumina Hi-C library. The resulting reference genome has a total of 1.1 Gb in length and was assembled into 10 chromosomes and 368 unplaced scaffolds, an N50 of 2.7 Mb, and a QV score of 43.58. The orthology analysis indicated high-quality with a 97.8% BUSCO completeness score and 36,149 annotated genes. 33% of the genome was identified as repeats and masked. The generation of the first soft tick reference genome establishes a basis for future studies to utilize genomic tools to support vector-borne disease management.

Deformed wing virus (DWV) has long been identified as a critical pathogen affecting honeybees, contributing to colony losses through wing deformities, neurological impairments, and reduced lifespan. Since DWV also affects other pollinators, it poses a significant threat to global pollination networks. While honeybees have been the focal point of DWV studies, emerging research indicates that this RNA virus is not host-specific but rather a generalist pathogen capable of infecting a wide range of insect species, including other bee species such as bumblebees and solitary bees, as well as wasps and ants. This expands the potential impact of DWV beyond honeybees to broader ecological communities. The black imported fire ant, Solenopsis richteri, is an economically important invasive ant species. In this study, we describe deformed wing (DW) symptoms in S. richteri. DW alates were found in three of nine (33%) laboratory colonies. The symptoms ranged from severely twisted wings to a single crumpled wing tip. Additionally, numerous symptomatic alates also displayed altered mobility, ranging from an ataxic gait to an inability to walk. Viral replication of DWV was confirmed using a modified strand-specific RT-PCR. Our results suggest that S. richteri can be an alternative host for DWV, expanding our understanding of DWV as a generalist pathogen in insects. However, additional research is required to determine whether DWV is the etiological agent responsible for DW syndrome in S. richteri.

The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the genome using high-fidelity long-read sequencing. This resulted in a highly contiguous contig assembly with 90% of the genome in 10 contigs. The contig assembly was placed in a chromosomal context using synteny with a closely related species, Anastrepha ludens, as both are members of the Anastrepha fraterculus group. The resulting assembly represents the five autosomes and the X chromosome which represents 95.9% of the genome, and 199 unplaced contigs representing the remaining 4.1%. Orthology analysis across the structural annotation sets of high quality tephritid genomes demonstrates the gene annotations are robust, and identified genes unique to Anastrepha species that may help define their pestiferous nature that can be used as a starting point for comparative genomics. This genome assembly represents the first of this species and will serve as a foundation for future genetic and genomic research in support of its management as an agricultural pest.

The Hunt bumble bee, Bombus huntii, is a widely distributed pollinator in western North America. The species produces large colony sizes in captive rearing conditions, experiences low parasite and pathogen loads, and has been demonstrated to be an effective pollinator of tomatoes grown in controlled environment agriculture systems. These desirable traits have galvanized producer efforts to develop commercial Bombus huntii colonies for growers to deliver pollination services to crops. To better understand Bombus huntii biology and support population genetic studies and breeding decisions, we sequenced and assembled the Bombus huntii genome from a single haploid male. High-fidelity sequencing of the entire genome using PacBio, along with HiC sequencing, led to a comprehensive contig assembly of high continuity. This assembly was further organized into a chromosomal arrangement, successfully identifying 18 chromosomes spread across the 317.4 Mb assembly with a BUSCO score indicating 97.6% completeness. Synteny analysis demonstrates shared chromosome number (n = 18) with Bombus terrestris, a species belonging to a different subgenus, matching the expectation that presence of 18 haploid chromosomes is an ancestral trait at least between the subgenera Pyrobombus and Bombus sensu stricto. In conclusion, the assembly outcome, alongside the minimal tissue sampled destructively, showcases efficient techniques for producing a comprehensive, highly contiguous genome.

The Mexican fruit fly, Anastrepha ludens, is a polyphagous true fruit fly (Diptera: Tephritidae) considered 1 of the most serious insect pests in Central and North America to various economically relevant fruits. Despite its agricultural relevance, a high-quality genome assembly has not been reported. Here, we described the generation of a chromosome-level genome forthe A. ludens using a combination of PacBio high fidelity long-reads and chromatin conformation capture sequencing data. The final assembly consisted of 140 scaffolds (821 Mb, N50 = 131 Mb), containing 99.27% complete conserved orthologs (BUSCO) for Diptera. We identified the sex chromosomes using 3 strategies: (1) visual inspection of Hi-C contact map and coverage analysis using the HiFi reads, (2) synteny with Drosophila melanogaster, and (3) the difference in the average read depth of autosomal vs sex chromosomal scaffolds. The X chromosome was found in 1 major scaffold (100 Mb) and 8 smaller contigs (1.8 Mb), and the Y chromosome was recovered in 1 large scaffold (6.1 Mb) and 35 smaller contigs (4.3 Mb). Sex chromosomes and autosomes showed considerable differences of transposable elements and gene content. Moreover, evolutionary rates of orthologs of A. ludens and Anastrepha obliqua revealed a faster evolution of X-linked, compared with autosome-linked, genes, consistent with the faster-X effect, leading us to new insights on the evolution of sex chromosomes in this diverse group of flies. This genome assembly provides a valuable resource for future evolutionary, genetic, and genomic translational research supporting the management of this important agricultural pest.

Commercial culture of channel catfish (Ictalurus punctatus) occurs in earthen ponds that are characterized by diel swings in dissolved oxygen concentration that can fall to severe levels of hypoxia, which can suppress appetite and lead to suboptimal growth. Given the significance of the hypothalamus in regulating these processes in other fishes, an investigation into the hypothalamus transcriptome was conducted to identify specific genes and expression patterns responding to hypoxia. Channel catfish in normoxic water were compared with catfish subjected to 12 h of hypoxia (20% oxygen saturation; 1.8 mg O2/L; 27°C) followed by 12 h of recovery in normoxia to mimic 24 h in a catfish aquaculture pond. Fish were sampled at 0-, 6-, 12-, 18-, and 24-h timepoints, with the 6- and 12-h samplings occurring during hypoxia. A total of 190 genes were differentially expressed during the experiment, with most occurring during hypoxia and returning to baseline values within 6 h of normoxia. Differentially expressed genes were sorted by function into Gene Ontology biological processes and revealed that most were categorized as "response to hypoxia," "sprouting angiogenesis," and "cellular response to xenobiotic stimulus." The patterns of gene expression reported here suggest that transcriptome responses to hypoxia are broad and quickly reversibly with the onset of normoxia. Although no genes commonly reported to modulate appetite were found to be differentially expressed in this experiment, several candidates were identified for future studies investigating the interplay between hypoxia and appetite in channel catfish, including adm, igfbp1a, igfbp7, and stc2b.NEW & NOTEWORTHY Channel catfish are an economically important species that experience diel episodic periods of hypoxia that can reduce appetite. This is the first study to investigate their transcriptome from the hypothalamus in a simulated 24-h span in a commercial catfish pond, with 12 h of hypoxia and 12 h of normoxia. The research revealed functional groups of genes relating to hypoxia, angiogenesis, and glycolysis as well as individual target genes possibly involved in appetite regulation.