Jason Johns, Malia L Moore, Merly Escalona, Courtney Miller, Noravit Chumchim, Oanh Nguyen, Mohan P A Marimuthu, Colin W Fairbairn, Eric Beraut, William E Seligmann, Samuel Sacco, Erin Toffelmier, H Bradley Shaffer, Todd P Michael, Scott Hodges
{"title":"A chromosome level genome assembly of the marine flowering plant, Torrey's surfgrass (Phyllospadix Torreyi) reveals an exceptionally large Y-chromosome.","authors":"Jason Johns, Malia L Moore, Merly Escalona, Courtney Miller, Noravit Chumchim, Oanh Nguyen, Mohan P A Marimuthu, Colin W Fairbairn, Eric Beraut, William E Seligmann, Samuel Sacco, Erin Toffelmier, H Bradley Shaffer, Todd P Michael, Scott Hodges","doi":"10.1093/jhered/esaf097","DOIUrl":"10.1093/jhered/esaf097","url":null,"abstract":"<p><p>Phyllospadix spp. (surfgrass) are flowering plants and keystone species in the rocky intertidal and subtidal environments of the North Pacific Ocean. Here we report a chromosome level assembly for P. torreyi, which occurs along the coast of California, sometimes in sympatry with P. scouleri. Both of these species and their putative hybrids are being studied as part of the California Conservation Genomics Project. Phyllospadix are dioecious, and males are exceptionally rare compared to females. Using high throughput, long reads (PacBio) and chromatin capture (Omni-C), we assembled a chromosome level genome for a male individual and a contig level assembly for a female individual. Comparison between the male and female assembly confirmed that the male is the heterogametic sex and has a massive Y chromosome at 124.8 megabases, which encompasses over 27% of the male genome. We also compared the male P. torreyi assembly to a genome from its sister genus, the monoecious Zostera marina, and found relatively high levels of synteny, that syntenic gene blocks on the P. torreyi sex chromosomes align to a single chromosome of Z. marina, and an estimated divergence time of ca. 25 million years ago. The Phyllospadix genome will be a powerful tool for studying marine dispersal, sex ratios, genetic diversity, sex chromosome evolution, and other dynamics in a keystone marine species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"566-576"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145566437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Reference genome of an irruptive migrant, the pine siskin (Spinus pinus).","authors":"Jair Cortez, Joel W G Slade, Tricia A Van Laar","doi":"10.1093/jhered/esaf076","DOIUrl":"10.1093/jhered/esaf076","url":null,"abstract":"<p><p>Pine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de novo using long-read sequencing and scaffolded with a reference-guided approach. Synteny analyses also showed that our assembly can reliably reveal genomic rearrangements relative to other finches. Using reference-based annotation, we identified thousands of protein-coding genes, including loci relevant to metabolism and immune function that demonstrate the utility of this assembly for downstream studies. We also found evidence of gene duplications and pseudogenization in immune loci, showing the utility of our assembly for immunogenetic studies. Our analysis provides the first genome-wide view of transposable element (TE) activity in Spinus, revealing multiple bursts of long terminal repeat (LTR) retrotransposon expansion, including a recent one that coincides with the estimated diversification of North and South American siskins approximately 2.7 million years ago. We also detected putative lineage-specific LTR sequences, suggesting recent or ongoing TE diversification. This assembly fills a critical gap in passerine genomic resources and provides a resource for comparative, transcriptomic, and population-level studies across species with diverse migratory strategies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"469-477"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wesley C Au, Kari A Morfeld, Christopher J Fields, Yasuko Ishida, Alfred L Roca
{"title":"Genomic Assessment of Giraffes in North American Collections Highlights Conservation Challenges.","authors":"Wesley C Au, Kari A Morfeld, Christopher J Fields, Yasuko Ishida, Alfred L Roca","doi":"10.1093/jhered/esaf089","DOIUrl":"10.1093/jhered/esaf089","url":null,"abstract":"<p><p>Recent genomics research has redefined the taxonomy of giraffes (genus Giraffa), identifying four distinct species rather than just one. This new understanding raises concerns about the ancestry of North American giraffe populations in human care (ex situ) and whether they still serve as meaningful conservation assurance populations for wild giraffe taxa. To address this, we performed whole-genome sequencing and analyses of 52 giraffes kept ex situ across North America, comparing them to wild giraffes representing all four recognized species. The analyses-including principal component analysis, admixture estimation, local ancestry inference, and mitochondrial phylogenetics-revealed extensive hybridization in giraffes kept ex situ. Most demonstrated mixed ancestry, primarily between northern and reticulated giraffes, with only a few individuals retaining un-admixed ancestries. Although some wild giraffes are known to be natural hybrids, overall there is strong reproductive isolation among giraffe species in the wild. Thus hybridization across species boundaries and potentially founder misclassification are responsible for the patterns observed ex situ. These findings highlight substantial genetic admixture in captivity, diminishing the conservation value of the current ex situ population. We recommend phasing out hybrid individuals from breeding programs and establishing new conservation-relevant stocks through collaboration with willing African governments and conservation organizations. Success will require coordinated international efforts and updates to global conservation frameworks, building on the formal recognition by the International Union for Conservation of Nature of distinct giraffe species and subspecies, to support taxon-specific conservation strategies that reflect the genetic distinctiveness of giraffe taxa.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"395-406"},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145380062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yasuko Ishida, Brian C Hamlin, Richard L Green, Emma C Schmidt, Brenna Freeman, Colin M Gillin, Alfred L Roca
{"title":"PRNP variant frequencies in Roosevelt and Rocky Mountain elk (Cervus canadensis) from Oregon and their implications for chronic wasting disease.","authors":"Yasuko Ishida, Brian C Hamlin, Richard L Green, Emma C Schmidt, Brenna Freeman, Colin M Gillin, Alfred L Roca","doi":"10.1093/jhered/esaf096","DOIUrl":"10.1093/jhered/esaf096","url":null,"abstract":"<p><p>Chronic wasting disease (CWD) is a fatal disease in cervids caused by abnormally folded proteins known as prions. Since its identification in 1967, CWD has spread to wild cervid populations in 36 US states. Some variants in the prion protein gene (PRNP) are known to confer advantages against prion diseases in many species including cervids. In elk (Cervus canadensis), a non-synonymous mutation in PRNP is associated with CWD susceptibility and/or progression. PRNP codon 132 L, which encodes leucine rather than methionine (132 M), is relatively less frequent among CWD positive elk than among CWD negative elk. In 2021, CWD was detected in Idaho near the Oregon border, heightening concerns about potential spread into Oregon's cervid populations. We therefore sequenced the complete coding region of PRNP in 183 elk collected across their range in Oregon, to assess PRNP variation. PRNP sequences have not previously been examined in the Roosevelt elk (Cervus canadensis roosevelti) subspecies. We assessed 101 Roosevelt elk in western Oregon, finding that 42% carried at least one copy of 132 L. Among Rocky Mountain elk (n = 82; Cervus elaphus nelsoni) in Oregon, 49% carried at least one copy of the advantageous allele 132 L. Oregon elk carry a relatively high proportion of 132 L compared with previously examined elk populations nationwide. Despite this high frequency, Oregon elk populations remain at substantial risk from CWD. These findings can inform management strategies aimed at mitigating CWD risk in Oregon's cervid populations.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"431-440"},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145544169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrey A Tomarovsky, Ruqayya Khan, Olga Dudchenko, Violetta R Beklemisheva, Polina L Perelman, Azamat A Totikov, Natalia A Serdyukova, Tatiana M Bulyonkova, Maria Pobedintseva, Alexei V Abramov, David Weisz, Aliya Yakupova, Anna Zhuk, Alexander S Graphodatsky, Roger Powell, Erez Lieberman Aiden, Klaus-Peter Koepfli, Sergei Kliver
{"title":"Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae).","authors":"Andrey A Tomarovsky, Ruqayya Khan, Olga Dudchenko, Violetta R Beklemisheva, Polina L Perelman, Azamat A Totikov, Natalia A Serdyukova, Tatiana M Bulyonkova, Maria Pobedintseva, Alexei V Abramov, David Weisz, Aliya Yakupova, Anna Zhuk, Alexander S Graphodatsky, Roger Powell, Erez Lieberman Aiden, Klaus-Peter Koepfli, Sergei Kliver","doi":"10.1093/jhered/esaf101","DOIUrl":"10.1093/jhered/esaf101","url":null,"abstract":"<p><p>The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (Martes zibellina zibellina), the Ural pine marten (Martes martes uralensis), and the Far East yellow-throated marten (Martes flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39 to 2.45 Gbp, N50 values of 137 to 145 Mbp, and high BUSCO scores (93.6% to 96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n = 38 and 2n = 40, respectively). Annotation predicted ~ 20,000 protein-coding genes per genome, of which > 90% were assigned functional names. Repeats encompass 36.9% to 40.4% of the assemblies, with a prevalence of LINEs and SINEs, and are conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verify a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"583-591"},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145688649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Terrence Sylvester, Richard Adams, Robert F Mitchell, Rongrong Shen, Duane D McKenna
{"title":"Genomic architecture of the pole borer, Neandra brunnea (Cerambycidae: Parandrinae), sheds light on the evolution of wood-feeding in longhorn beetles.","authors":"Terrence Sylvester, Richard Adams, Robert F Mitchell, Rongrong Shen, Duane D McKenna","doi":"10.1093/jhered/esaf080","DOIUrl":"10.1093/jhered/esaf080","url":null,"abstract":"<p><p>Neandra brunnea, commonly known as the pole borer, is a species of wood-boring (xylophagous) longhorn beetle (family Cerambycidae) found throughout most of eastern North America. We sequenced, assembled, and annotated the genome of N. brunnea and compared it to publicly available genomes of other Cerambycidae. The 1.23 Gb N. brunnea genome assembly was distributed across 78 contigs, with an N50 of 38.88 Mb and largest contig of 74.28 Mb. Most of the genome was comprised of repetitive sequences, with 81.39% comprising interspersed repeats. Most (99.7%) of the expected orthologous genes (BUSCOs) were present and fully assembled, with only 2.5% duplicated. The genome annotation identified 13 003 genes (15 574 transcripts), including 301 putative horizontally transferred loci from a diversity of both prokaryotic and eukaryotic donors. The assembled mitochondrial genome is relatively large at 17 kb and shows an unusual repeating array of d-loop segments. As the first representative of the longhorn beetle subfamily Parandrinae with a sequenced genome, N. brunnea provides an important new point of reference for the comparative study of beetle genomes and a further resource for studies of the evolution and genomic basis of xylophagy.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"492-501"},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cicero Alves-Lima, Gabriel Montecinos, Merly Escalona, Sara Calhoun, Mohan Marimuthu, Oanh Nguyen, Eric Beraut, Anna Lipzen, Igor V Grigoriev, Peter Raimondi, Sergey Nuzhdin, Filipe Alberto
{"title":"The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana.","authors":"Cicero Alves-Lima, Gabriel Montecinos, Merly Escalona, Sara Calhoun, Mohan Marimuthu, Oanh Nguyen, Eric Beraut, Anna Lipzen, Igor V Grigoriev, Peter Raimondi, Sergey Nuzhdin, Filipe Alberto","doi":"10.1093/jhered/esaf077","DOIUrl":"10.1093/jhered/esaf077","url":null,"abstract":"<p><p>Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with a broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of N. luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80× of coverage, and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and Macrocystis pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPase enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"478-491"},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145281960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
William Maguire, Mattheau Comerford, Lily Shiue, Qianyu Jin, Gina Wimp, Shannon Murphy, Brook Moyers, Mayra C Vidal
{"title":"Improved, annotated reference genome for the highly polyphagous moth Hyphantria cunea (Fall webworm).","authors":"William Maguire, Mattheau Comerford, Lily Shiue, Qianyu Jin, Gina Wimp, Shannon Murphy, Brook Moyers, Mayra C Vidal","doi":"10.1093/jhered/esaf099","DOIUrl":"10.1093/jhered/esaf099","url":null,"abstract":"<p><p>Fall webworm (Hyphantria cunea) is a widespread, highly polyphagous moth in the family Erebidae, whose native range spans much of North America and invasive range includes Asia and Europe. The species uses over 600 plant species as a larval host, making it among the most generalized insect herbivores described. Its variable host use, wide range, and genetic diversity make fall webworm an attractive emerging model system for the study of diet breadth, but studies have been limited by the lack of a high-quality annotated reference genome. Here we report an annotated, chromosome-scale genome of much improved continuity and completeness over the previously available unannotated fall webworm reference genome. We used PacBioHiFi long reads and Omni-C proximity ligation sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus and third in the family, contains 321 scaffolds spanning 0.572 gigabases with a N50 of 14.6 Mb and BUSCO complete score of 99.1%. This genome will represent a valuable resource for research into the ecology, evolution, and genetics of dietary generalism and diet breadth in insect herbivores.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"577-582"},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145607151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Low genetic diversity of major histocompatibility complex class II DQB gene in wild rhesus and long-tailed macaques in Thailand reflects purifying selection and poses risks to population health.","authors":"Worapong Singchat, Wongsathit Wongloet, Trifan Budi, Thitipong Panthum, Aingorn Chaiyes, Kornsuang Jangtarwan, Prateep Duengkae, Sunchai Payungporn, Suthirote Meesawat, Taratorn Kemthong, Yuzuru Hamada, Suchinda Malaivijitnond, Kornsorn Srikulnath","doi":"10.1093/jhered/esaf100","DOIUrl":"10.1093/jhered/esaf100","url":null,"abstract":"<p><p>Rhesus (Macaca mulatta) and long-tailed (M. fascicularis) macaques, important for biomedical research, are distributed across Thailand, and hybridization and introgression between species influence genetic diversity, potentially leading to variability in traits and pathogen susceptibility. Elucidation of the genetic components directly related to pathogen susceptibility, such as major histocompatibility complex genes (MHC) across different environmental conditions, is crucial. Thus, this study examined the MHC class II DQB diversity in 18 populations of wild rhesus and long-tailed macaques in Thailand. Next-generation sequencing was used to screen 298 bp partial exon 2 of DQB. Habitat suitability was analyzed using Maximum Entropy Modeling to identify the main factors affecting macaque distribution, which may relate to allelic diversity. Six alleles (Mamu-Mafa-DQB1*TH01-Mamu-Mafa-DQB1*TH06) were observed in both species, with no evidence of species-specific alleles. Two alleles (Mamu-Mafa-DQB1*TH05 and Mamu-Mafa-DQB1*TH06) were restricted to two Northeastern populations. Selection analysis indicated that purifying selection acted on the MHC gene pool. Northeastern Thailand was identified as a suitable habitat for rhesus macaques, with the distance to roads as a primary predictor. Central to southern Thailand, with its elevation and distance to rivers, was predicted to be suitable for long-tailed macaques. The homozygous genotype of Mamu-Mafa-DQB1*TH02 allele was found in all individuals of one long-tailed macaque population, resulting in an increased risk of poor population health and pathogen infection. This study provides insights into the evolution of Thai macaques with potential implications for their use in biomedical research, such as disease susceptibility and resistance, as well as in vaccine development.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"417-430"},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
William T McMahan, Merly Escalona, Reed Kenny, Mohan P A Marimuthu, Oanh Nguyen, Colin W Fairbairn, William Seligmann, Courtney Miller, Howard Bradley Shaffer, Shannon Still, Daniel Potter
{"title":"\"A genome assembly of the California flannelbush, Fremontodendron californicum\".","authors":"William T McMahan, Merly Escalona, Reed Kenny, Mohan P A Marimuthu, Oanh Nguyen, Colin W Fairbairn, William Seligmann, Courtney Miller, Howard Bradley Shaffer, Shannon Still, Daniel Potter","doi":"10.1093/jhered/esaf105","DOIUrl":"10.1093/jhered/esaf105","url":null,"abstract":"<p><p>Fremontodendron (Malvaceae) is a genus of shrubs native to the California Floristic Province (CFP) with dense, stellate trichomes on their leaves (hence the common name \"flannelbush\"). The current treatment of the genus includes the widespread and morphologically variable species Fremontodendron californicum, along with the rare F. decumbens and F. mexicanum. While F. californicum is spread across several ecoregions of the CFP, F. decumbens and F. mexicanum are highly restricted. Here, we introduce the first genome-scale resource with which to study this important genus, a de novo, scaffold scale assembly of an individual of F. californicum. Following the overall strategy of the California Conservation Genomics Project (CCGP), we used Pacific Biosciences HiFi long reads and Omni-C chromatin mapping to produce an assembly of the nuclear and plastid (chloroplast) genomes. The nuclear assembly consists of two, phased haplotypes, haplotypes one and two, with similar sizes of around 1.2 Gb, similar scaffold N50s around 26 Mb, and each with a Benchmarking Universal Single-Copy Ortholog (BUSCO) completeness score of 99.4%. This assembly will be a valuable resource for understanding the distribution, genetic variation, and species delimitation of this California genus of conservation value, as well as a tool to further investigate the complex evolutionary history of Malvaceae s.l.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"600-610"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145758283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}