Journal of Heredity最新文献_第10页

Chromosome-level genome assembly of the sacoglossan sea slug Elysia atroviridis. 棘海蛞蝓atroviridis染色体水平的基因组组装。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2026-05-13 DOI: 10.1093/jhered/esag037

BingYu Guo, LingFeng Kong

{"title":"Chromosome-level genome assembly of the sacoglossan sea slug Elysia atroviridis.","authors":"BingYu Guo, LingFeng Kong","doi":"10.1093/jhered/esag037","DOIUrl":"https://doi.org/10.1093/jhered/esag037","url":null,"abstract":"Some sacoglossan sea slugs (Gastropoda:Heterobranchia) possess the remarkable ability to sequester functional chloroplasts into digestive cells. Elysia atroviridis harvests chloroplasts from its algal prey, which are maintained for a relative long period in cells of the digestive tract. We successfully assembled a high-quality chromosome-level genome of E. atroviridis using PacBio and Hi-C sequencing technologies. The final assembly spans 829.0 Mb with contig and scaffold N50 length of 2.0 Mb and 43.9 Mb, respectively, 89.3% of the assembled sequences were anchored to 15 pseudochromosomes. We found no evidence for horizontal gene transfer (HGT), specifically, no photosynthetic genes encoded in the E. atroviridis nucleus genome. A total of 16,472 protein-coding genes were predicted, of which 96.0% were functionally annotated. Phylogenetic analysis indicated E. atroviridis and E. timida formed a clade and their divergence time was estimated approximately 33 million years ago (Mya). Collinearity analysis revealed a high level of synteny with the genome of both species. This genome provides a valuable resource for further investigation into the evolution and mechanisms of kleptoplasty in sacoglossa.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147935534","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}

引用次数: 0

A near chromosome-scale genome assembly of the common pine sawfly (Diprion Pini). 常见松锯蝇（Diprion Pini）的近染色体尺度基因组组装。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2026-05-11 DOI: 10.1093/jhered/esag039

Saskia Wutke, Craig Michell, Carita Lindstedt

{"title":"A near chromosome-scale genome assembly of the common pine sawfly (Diprion Pini).","authors":"Saskia Wutke, Craig Michell, Carita Lindstedt","doi":"10.1093/jhered/esag039","DOIUrl":"https://doi.org/10.1093/jhered/esag039","url":null,"abstract":"The common pine sawfly, Diprion pini, is a widespread defoliator of pine forests across Europe and Asia, with outbreaks causing substantial ecological and economic damages. However, genomic resources for this species have been limited, hindering advances in molecular ecology or pest management. Here, we present a near chromosome-level reference genome for D.pini, generated using PacBio HiFi reads, Oxford Nanopore MionION long reads, and 10× Genomics linked reads. The final assembly is organized into mostly chromosome-sized scaffolds. It spans a length of 268 Mb, comprises 81 scaffolds, and has a scaffold N50 of 18.7 Mb. BUSCO analysis (hymenoptera_odb10) indicates a high genome completeness of 97.2%. With 22,7 kb the mitochondrial genome is unusually large due to an extended non-coding control region (6874 bp). Gene prediction identified 26,335 protein-coding genes, of which 12,769 were functionally annotated. Comparative analyses with other sawflies and Apocrita identified 2472 proteins unique to D. pini, some of which are putatively associated with the processing of plant secondary metabolites. Notably, our genome assembly highlights that, when a closely related, high-quality reference genome is available, chromosome-scale assemblies can be generated without the need of Hi-C sequencing. The genome provides a valuable foundation for the development of improved monitoring and management strategies for D. pini outbreaks and contributes to advancing fundamental research on Hymenoptera evolution.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876637","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}

引用次数: 0

A chromosome-level genome assembly of the forked fungus beetle Bolitotherus cornutus, a model system for studying social evolution in the wild. 分叉真菌甲虫Bolitotherus cornutus的染色体水平基因组组装，这是研究野生社会进化的模式系统。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf071

Kyle M Benowitz, Zachery M Esterline, Allina A Win, Vincent A Formica, Edmund D Brodie Iii

引用次数: 0

Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus). 挪威野生高山驯鹿（Rangifer tarandus tarandus）染色体水平的基因组组装。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf094

Ole K Tørresen, Ave Tooming-Klunderud, Morten Skage, Anne Eline Streitlien, Olav Strand, Christer M Rolandsen, Giada Ferrari, José Cerca, Atle Mysterud, Kjetill S Jakobsen

引用次数: 0

A high-quality reference genome for the ornate shrew (Sorex ornatus). 华丽鼩鼱（Sorex ornatus）的高质量参考基因组。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf074

Isaac J Linn, Merly Escalona, Oanh Nguyen, Mohan P A Marimuthu, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Eric Beraut, Christopher J Conroy, Rauri C K Bowie, Michael W Nachman

引用次数: 0

Transcriptomics of feeding and reproductive stages of the South American cactus moth. 南美仙人掌蛾摄食和繁殖阶段的转录组学。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf091

Daniel Poveda-Martínez, Nicolás Nahuel Moreyra, Jose Manuel Latorre Estivalis, Esteban Hasson, Laura Varone

{"title":"Transcriptomics of feeding and reproductive stages of the South American cactus moth.","authors":"Daniel Poveda-Martínez, Nicolás Nahuel Moreyra, Jose Manuel Latorre Estivalis, Esteban Hasson, Laura Varone","doi":"10.1093/jhered/esaf091","DOIUrl":"10.1093/jhered/esaf091","url":null,"abstract":"The cactus moth, Cactoblastis cactorum, native to southern South America, has extended its range throughout Florida, north to coastal South Carolina and west to Texas in the United States and the Caribbean region, posing a threat to native Opuntia and also affecting the production of prickly pear-associated industries in both its native and non-native ranges. Past efforts to control the cactus moth have not been effective. However, promising biological control agents are currently under evaluation. Moreover, as genomic and transcriptomic data become available, emerging techniques, such as gene editing, offer promising avenues for developing alternative control strategies. In this study, we present novel transcriptomic data of adult male and female moths and larvae using RNA-Seq to gain new insights into the genetic repertoire of this cactus pest along its life cycle. The final assembly revealed 14,202 genes, of which 2,199 and 2,008 transcripts were differentially expressed between males and females, and between larvae and adults, respectively. Overall, functional analyses pointed to an enrichment of serine-type peptidase inhibitors, odorant-binding proteins, and glycoside hydrolases between life cycle stages (larvae vs. adults) and sex-specific biological functions. Our study provides the first report of differential gene expression across developmental stages, generating new and valuable genetic resources to guide future molecular and physiological research as well as pest management strategies in the cactus moth.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"407-416"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145423452","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}

引用次数: 0

A genome assembly for mule deer, Odocoileus hemionus, from Southern California. 来自南加州的骡鹿的基因组组装。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf082

Joshua M Hallas, Samantha L R Capel, Merly Escalona, Oanh Nguyen, Samuel Sacco, Ruta Sahasrabudhe, William Seligmann, Benjamin N Sacks, Michael R Buchalski

{"title":"A genome assembly for mule deer, Odocoileus hemionus, from Southern California.","authors":"Joshua M Hallas, Samantha L R Capel, Merly Escalona, Oanh Nguyen, Samuel Sacco, Ruta Sahasrabudhe, William Seligmann, Benjamin N Sacks, Michael R Buchalski","doi":"10.1093/jhered/esaf082","DOIUrl":"10.1093/jhered/esaf082","url":null,"abstract":"Mule deer (Odocoileus hemionus) is an ecologically and economically important cervid species which is widely distributed across western North America. Their broad range and use of diverse habitats, including those linked to historical glacial refugia, have made them an ideal model for studying the effects of climatic fluctuations and environmental heterogeneity on lineage diversification. The effects of this complex evolutionary history on the genome are further complicated by evidence of hybridization with other members of the genus, leading to extreme cases of mito-nuclear discordance. More recently, the influence of specific gene variants on disease dynamics, particularly the progression and morbidity of chronic wasting disease, has become an important topic of genomic research for this taxon. Here, we present and evaluate a new chromosome-level genome assembly of a representative mule deer from across the species' diverse range as part of the California Conservation Genomics Project. We assembled a genome de novo utilizing Pacific Biosciences HiFi long-read and Omni-C chromatin-proximity sequencing data. The assembly consisted of 814 scaffolds and 901 contigs representing a contig N50 of 46.68 Mb and a scaffold N50 of 63.29 Mb. Lastly, our benchmarking universal single-copy ortholog completeness score was 96.3%. This genome represents one of the most complete Odocoileus assemblies and will further our understanding of the comparative genomic architecture of cervids.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"502-511"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145304414","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}

引用次数: 0

De novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing. 通过长读Oxford Nanopore MinION测序对全球入侵的绿岸蟹Carcinus maenas （Linnaeus, 1758）进行从头全基因组组装。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf085

Jolanda K Brons, Thomas Hackl, Riccardo Iacovelli, Kristina Haslinger, Sebastian Lequime, Sancia E T van der Meij

{"title":"De novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing.","authors":"Jolanda K Brons, Thomas Hackl, Riccardo Iacovelli, Kristina Haslinger, Sebastian Lequime, Sancia E T van der Meij","doi":"10.1093/jhered/esaf085","DOIUrl":"10.1093/jhered/esaf085","url":null,"abstract":"Invasive species are reshaping aquatic ecosystems worldwide at an accelerating pace, with profound ecological and economic impacts. Many crustacean species have demonstrated invasive potential or are already well-established invaders. The green shore crab, Carcinus maenas, native to Europe and North Africa, is one of the most successful global marine invaders and is now present on six continents. Although the role of genomics in invasion science is increasingly recognized, genomic resources for brachyuran crabs remain limited, including the notable absence of a reference genome for C. maenas. Here we report on a de novo whole genome assembly of C. maenas via long-read Oxford Nanopore Technology sequencing. The assembly spans 1.09 Gbp across 21 887 scaffolds (NG50 = 13 Mbp) with a BUSCO completeness of 98.4%, providing a high-quality resource for future genomic analyses. We provide a detailed protocol for obtaining high-quality DNA to successfully sequence brachyuran crabs using a long-read approach. This new resource expands available genomic data for the species-rich infraorder Brachyura, and provides a valuable foundation for understanding the genetic factors underlying the global invasion success of C. maenas, supporting future research in marine invasion genomics.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"537-544"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145349975","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}

引用次数: 0

Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal (Mirounga angustirostris). 一种深潜鳍足象海豹的基因组组装和注释。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf083

Milagros G Rivera, Merly Escalona, John Carlos Garza, Courtney Miller, Eric Beraut, Colin Fairbairn, Samuel Sacco, William E Seligmann, Ruta Sahasrabudhe, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Daniel P Costa, Roxanne S Beltran, Rachel S Meyer

{"title":"Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal (Mirounga angustirostris).","authors":"Milagros G Rivera, Merly Escalona, John Carlos Garza, Courtney Miller, Eric Beraut, Colin Fairbairn, Samuel Sacco, William E Seligmann, Ruta Sahasrabudhe, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Daniel P Costa, Roxanne S Beltran, Rachel S Meyer","doi":"10.1093/jhered/esaf083","DOIUrl":"10.1093/jhered/esaf083","url":null,"abstract":"The northern elephant seal (Mirounga angustirostris) is the largest pinniped species in the northern hemisphere. The species is classified as being of least conservation concern by the IUCN-a triumph of conservation efforts despite hunting pressure that nearly led to its extinction more than a century ago. The historical range of the northern elephant seal extended from Baja California to Alaska, but overexploitation caused a severe demographic collapse and genetic bottleneck, with only an estimated 10 to 30 survivors left on Isla Guadalupe, Mexico. As part of the California Conservation Genomics Project, we generated a de novo reference genome and annotation for M. angustirostris, combining PacBio HiFi long-read sequencing data with Dovetail Omni-C chromatin conformation data. Our assembly has a primary haplotype genome length of 2,430,321,998 base pairs (2.4 Gb), with the longest contig of 144 Mb, contig N50 of 58 Mb, largest scaffold of 215 Mb, and scaffold N50 of 154 Mb. The secondary assembly haplotype consists of 422 scaffolds, spanning 2.45 Gb, with contig N50 of 61.24 Mb, scaffold N50 of 152.94 Mb, the largest contig of 204.14 Mb, and the largest scaffold of 216.16 Mb. We used the primary assembly and annotation for a preliminary investigation of repeat element content, historical demography, genome-wide heterozygosity, and loss-of-function variants. We found that M. angustirostris has one of the lowest estimates of genetic diversity of any marine mammal and a complex demographic history that may have reduced genetic diversity several times. This newly constructed genome will facilitate future in-depth explorations into the mechanisms behind resilience and recovery after a severe population bottleneck.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"512-525"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145379985","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}

引用次数: 0

Genomic resources for comparative analyses of avian obligate brood parasitism. 专性雏鸟寄生比较分析的基因组资源。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-05-06 DOI: 10.1093/jhered/esaf087

Rachel A Carroll, Edward S Ricemeyer, LaDeana W Hillier, Jeffrey M DaCosta, Ekaterina Osipova, Sara Smith, Gabriel A Jamie, Juan G Martinez, Mercedes Molina-Morales, Tomas Marques-Bonet, Joseph D Manthey, Diana Haddad, Matthew J Fuxjager, Kathleen S Lynch, Jonathan M D Wood, Erich Jarvis, Patrick Masterson, Francoise Thibaud-Nissen, Mark E Hauber, Claire N Spottiswoode, Timothy B Sackton, Christopher N Balakrishnan, Michael D Sorenson, Wesley C Warren

{"title":"Genomic resources for comparative analyses of avian obligate brood parasitism.","authors":"Rachel A Carroll, Edward S Ricemeyer, LaDeana W Hillier, Jeffrey M DaCosta, Ekaterina Osipova, Sara Smith, Gabriel A Jamie, Juan G Martinez, Mercedes Molina-Morales, Tomas Marques-Bonet, Joseph D Manthey, Diana Haddad, Matthew J Fuxjager, Kathleen S Lynch, Jonathan M D Wood, Erich Jarvis, Patrick Masterson, Francoise Thibaud-Nissen, Mark E Hauber, Claire N Spottiswoode, Timothy B Sackton, Christopher N Balakrishnan, Michael D Sorenson, Wesley C Warren","doi":"10.1093/jhered/esaf087","DOIUrl":"10.1093/jhered/esaf087","url":null,"abstract":"Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6-4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"545-556"},"PeriodicalIF":2.2,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145423468","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}

引用次数: 0