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1. A haplotype-resolved, chromosome-scale genome for Malus domestica Borkh. ‘WA 38’

   https://doi.org/10.1093/g3journal/jkae222  

   Zhang, Huiting; Ko, Itsuhiro; Eaker, Abigail; Haney, Sabrina; Khuu, Ninh; Ryan, Kara; Appleby, Aaron B; Hoffmann, Brendan; Landis, Henry; Pierro, Kenneth A; et al (September 2024, G3: Genes, Genomes, Genetics)

   McIntyre, L (Ed.)

   Abstract Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation give breeders, researchers, and growers information about cultivar-specific traits such as fruit quality and disease resistance, and inform strategies to enhance postharvest storage. Here we present a haplotype-phased, chromosomal-level genome of Malus domestica, ‘WA 38’, a new apple cultivar released to market in 2017 as Cosmic Crisp®. Using both short and long-read sequencing data with a k-mer-based approach, chromosomes originating from each parent were assembled and segregated. This is the first pome fruit genome fully phased into parental haplotypes in which chromosomes from each parent are identified and separated into their unique, respective haplomes. The two haplome assemblies, ‘Honeycrisp’ originated HapA and ‘Enterprise’ originated HapB, are about 650 Megabases each, and both have a BUSCO score of 98.7% complete. A total of 53,028 and 54,235 genes were annotated from HapA and HapB, respectively. Additionally, we provide genome-scale comparisons to ‘Gala’, ‘Honeycrisp’, and other relevant cultivars highlighting major differences in genome structure and gene family circumscription. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that includes ‘WA 38’ (Washington State University), ‘d’Anjou’ pear (Auburn University), and many more. To ensure transparency, reproducibility, and applicability for any genome project, our genome assembly and annotation workflow is recorded in detail and shared under a public GitLab repository. All software is containerized, offering a simple implementation of the workflow. 

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2. SpudDB: a database for accessing potato genomic data

   https://doi.org/10.1093/genetics/iyae205  

   Hamilton, John P; Brose, Julia; Buell, C Robin (December 2024, GENETICS)

   Harris, T (Ed.)

   Abstract Potato is a key food crop with a complex, polyploid genome. Advancements in sequencing technologies coupled with improvements in genome assembly algorithms have enabled generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato. The SpudDB database houses potato genome sequence and annotation, with the doubled monoploid DM 1–3 516 R44 (hereafter DM) genome serving as the reference genome and haplotype. Diverse annotation data types for DM genes are provided through a suite of Gene Report Pages including gene expression profiles across 438 potato samples. To further annotate potato genes based on expression, 65 gene co-expression modules were constructed that permit the identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress. Genome browser views of DM and 28 other potato genomes are provided along with a download page for genome sequence and annotation. To link syntenic genes within and between haplotypes, syntelogs were identified across 25 cultivated potato genomes. Through access to potato genome sequences and associated annotations, SpudDB can enable potato biologists, geneticists, and breeders to continue to improve this key food crop. 

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3. A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

   https://doi.org/10.64898/2025.12.19.695579  

   Shan, Shengchen; Ortiz, Edgardo M; Klein, Baylee; Oganisyan, Arthur; Serrano, Gia; Stults, Bryanna; Torkzadeh, Rubina; Tucker, Audrey; Linnan, Ezra; Pringle, Benjamin; et al (December 2025, bioRxiv)

   Abstract Carya glabra(2n= 4x= 64), also known as pignut hickory, is a widely distributed species in the walnut family (Juglandaceae). Native to the central and eastern United States and southeastern Canada,C. glabraplays an important ecological role as a common upland forest species; it is closely related to several economically valuable nut trees, includingC. illinoinensis(pecan). A deeper understanding of the genetics ofC. glabrais essential for studying its evolutionary history and biology, with potential implications for agricultural improvement of pecan. Here, we present the first nuclear genome assembly and annotation ofC. glabra. The assembly is chromosome-level and phased, representing the first assembled polyploid genome in the genusCarya. A total of 64 pseudochromosomes were assembled and phased into four haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Functional annotation assigned 94.3% of haplotype A genes to gene families, and 79.7% and 86.3% of genes were annotated with Gene Ontology terms and protein domains, respectively; 635 putative plant disease resistance genes were found in haplotype A. The other three haplotypes exhibited similarly high-quality annotation metrics. Our genomic analyses also suggest thatC. glabrais an autotetraploid. Comparative genomic analyses revealed high collinearity among the four haplotypes ofC. glabraand the published genomes of three otherCaryaspecies, although structural variation among the genomes of these species was identified. In addition, we provide an improved chloroplast genome assembly and the first mitochondrial genome forC. glabra. Importantly, most members of the research team are undergraduate students; the sequenced individual is located in McCarty Woods, a Conservation Area on the University of Florida campus. This work highlights the value of genome assembly efforts as powerful tools for teaching genomics and supporting conservation initiatives. This first high-quality reference genome forC. glabraprovides a valuable resource for studyingCarya, a genus of significant ecological and economic importance. Article summaryCarya glabra(pignut hickory) is a common upland forest species in North America. This species is a member of the walnut family (Juglandaceae), which includes many economically important nut trees. Here, we present the first nuclear genome assembly and annotation ofC. glabra. The assembly is chromosome-level and phased. The haplotype A assembly contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Our genomic analyses suggest thatC. glabrais an autopolyploid. We also provide chloroplast and mitochondrial genome assemblies. This nuclear genome provides a valuable resource for studyingCarya, a genus of significant ecological and economic importance. 

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4. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

   https://doi.org/10.1038/s41588-020-00723-9  

   Sun, Xuepeng; Jiao, Chen; Schwaninger, Heidi; Chao, C. Thomas; Ma, Yumin; Duan, Naibin; Khan, Awais; Ban, Seunghyun; Xu, Kenong; Cheng, Lailiang; et al (December 2020, Nature Genetics)

   null (Ed.)

   Abstract Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple ( Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris . Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality. 

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5. Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes

   https://doi.org/10.1038/s41437-025-00803-8  

   Moosman, Owen W; Kelley, Joanna L; Bogan, Samuel N (October 2025, Heredity)

   Abstract Phased genomes and pangenomes are enhancing our understanding of genetic variation. Accurate phasing and assembly in repetitive regions of the genome remain challenging, however. Addressing this obstacle is crucial for studying structural genomic variation, such as copy number variations (CNVs) common to repetitive regions. Polar fishes, for example, evolved repetitive tandem arrays of antifreeze protein (AFP) genes that facilitate adaptation to freezing and expanded in copy number in colder environments. AFP CNVs remain poorly characterized in polar fishes and may be illuminated by haplotype-aware approaches. We performed long-read sequencing for two polar fishes in the suborder Zoarcoidei and leveraged additional published long-read data to assemble phased genomes. We developed a workflow to measure haplotype diversity in CNV while controlling for misassembly and switch errors—a change from one parental haplotype to another in a contiguous assembly. We presentgfa_parser, which computes and extracts all possible contiguous sequences for phased or primary assemblies from graphical fragment assembly (GFA) files, andswitch_error_screen, which flags potential switch errors.gfa_parserrevealed that assembly uncertainty was ubiquitous across AFP array haplotypes and that standard processing of graphical fragment assemblies can bias measurement of haplotype CNVs. We detected no switch errors in AFP arrays. After controlling for misassembly and switch error, we detected haplotype diversity of AFP CNVs in all studied polar Zoarcoidei species and in 60% of AFP arrays. Intraindividual haplotype diversity spanned differences of 3–16 copies. Our workflow revealed intraspecific genomic diversity in zoarcoids that likely fueled the evolution of AFP copy number across temperature. 

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