Journal of Heredity最新文献

Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri). 欧洲河七鳃鳗（Lampetra fluviatilis）和溪七鳃鳗（Lampetra planeri）全基因组组合的比较。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-13 DOI: 10.1093/jhered/esaf036

Ole K Tørresen, Benedicte Garmann-Aarhus, Siv Nam Khang Hoff, Sissel Jentoft, Mikael Svensson, Eivind Schartum, Ave Tooming-Klunderud, Morten Skage, Anders Krabberød, Leif Asbjørn Vøllestad, Kjetill S Jakobsen

{"title":"Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri).","authors":"Ole K Tørresen, Benedicte Garmann-Aarhus, Siv Nam Khang Hoff, Sissel Jentoft, Mikael Svensson, Eivind Schartum, Ave Tooming-Klunderud, Morten Skage, Anders Krabberød, Leif Asbjørn Vøllestad, Kjetill S Jakobsen","doi":"10.1093/jhered/esaf036","DOIUrl":"https://doi.org/10.1093/jhered/esaf036","url":null,"abstract":"We present haplotype-resolved whole-genome assemblies from one individual European river lamprey (Lampetra fluviatilis) and one individual brook lamprey (Lampetra planeri), usually regarded as sister species. The genome assembly of L. fluviatilis consists of pseudo-haplotype one, spanning 1073 Mb and pseudo-haplotype two, spanning 963 Mb. Likewise for the L. planeri specimen, the genome assembly spans 1049 Mb and 960 Mb for pseudo-haplotypes one and two, respectively. Both the L. fluviatilis pseudo-haplotypes have been scaffolded into 82 pseudo-chromosomes, with the same number for the L. planeri pseudo-haplotypes. All four pseudo-haplotype assemblies were annotated, identifying 21,479 and 16,973 genes in pseudo-haplotypes one and two for L. fluviatilis, and 24,961 and 21,668 genes in pseudo-haplotypes one and two for L. planeri. A comparison of the genomes of L. fluviatilis and L. planeri, alongside a separate chromosome level assembly of L. fluviatilis from the UK, indicates that they form a species complex, potentially representing distinct ecotypes. This is further supported by phylogenetic analyses of the three reference Lampetra genomes in addition to sea lamprey (Petromyzon marinus).","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287135","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

Chromosome-Level genome assembly and transcriptome analysis of the ural owl, Strix uralensis Pallas, 1771. 乌拉尔猫头鹰（Strix uralensis Pallas）染色体水平基因组组装和转录组分析。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-13 DOI: 10.1093/jhered/esaf038

Sven Winter, René Meißner, Martin Grethlein, Gerrit Wehrenberg, Angelika Kiebler, Andrea X Silva, Natalia Reyes Escobar, Suany M Quesada Calderón, Ana V Suescún, Luis Guzman Belmar, Stefan Prost

{"title":"Chromosome-Level genome assembly and transcriptome analysis of the ural owl, Strix uralensis Pallas, 1771.","authors":"Sven Winter, René Meißner, Martin Grethlein, Gerrit Wehrenberg, Angelika Kiebler, Andrea X Silva, Natalia Reyes Escobar, Suany M Quesada Calderón, Ana V Suescún, Luis Guzman Belmar, Stefan Prost","doi":"10.1093/jhered/esaf038","DOIUrl":"https://doi.org/10.1093/jhered/esaf038","url":null,"abstract":"The Ural owl (Strix uralensis) is a large member of the Strigidae family and inhabits Eurasian forests ranging from Germany to Japan. However, it faces increased range reduction, particularly at its southwestern distribution edges. Despite being considered 'Least Concern' by the IUCN, local populations have become threatened in Central Europe due to severe habitat loss. Reintroduction programs aim to restore these populations by closing distribution gaps and facilitating natural recolonization of suitable habitats. To support these efforts, genomic resources have become an established tool to assess genetic diversity, geographic structure, and potential inbreeding, crucial for maintaining the genetic health and adaptability of newly established populations. Here, we present a de novo genome assembly and transcriptome of the Ural owl based on ONT long-reads, Omni-C Illumina short-reads, and RNASeq data. The final assembly has a total length of 1.26 Gb, of which 96.42% is anchored into the 42 largest scaffolds. The scaffold and contig N50 values of 88.65 Mb and 21.74 Mb, respectively, a BUSCO/compleasm completeness of 97.5%/99.65% and k-mer completeness of 95.18%, emphasize the high quality of this assembly. Furthermore, annotation of the assembly identified 17 650 genes and a repeat content of 12.48%. This new highly contiguous and chromosome-level assembly will greatly benefit Ural owl conservation management by informing reintroduction programs about the species' genetic health and contributing a valuable resource to study genetic function in greater detail across the whole Strigidae family.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287085","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

Regional population genetics and global phylogeography of the widely distributed golden jackal (Canis aureus): Implications for conservation management. 分布广泛的金豺（Canis aureus）的区域种群遗传学和全球系统地理学：对保护管理的启示。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-12 DOI: 10.1093/jhered/esaf037

Yellapu Srinivas, Robert C Fleischer, Jesús E Maldonado, Malgorzata Pilot, Yadvendradev V Jhala

{"title":"Regional population genetics and global phylogeography of the widely distributed golden jackal (Canis aureus): Implications for conservation management.","authors":"Yellapu Srinivas, Robert C Fleischer, Jesús E Maldonado, Malgorzata Pilot, Yadvendradev V Jhala","doi":"10.1093/jhered/esaf037","DOIUrl":"https://doi.org/10.1093/jhered/esaf037","url":null,"abstract":"In the current era, many terrestrial carnivore populations confront a multitude of threats and are rapidly shifting their ranges in response to human-induced modifications. Monitoring changes in genetic diversity and structure of such species in response to changing environmental conditions is important for understanding species' responses and designing effective conservation management strategies. In this study, we investigated the genetic status of the golden jackal, a widely distributed canid inhabiting human-dominated landscapes and exhibiting high dispersal capability. We collected and analysed 141 jackal samples from across the distribution range in India, employing a combination of mtDNA (Cyt-b & CR) and nuclear microsatellite (n = 25) markers to investigate patterns of genetic diversity, gene flow, demographic history and phylogeography. Our analyses showed substantial levels of genetic diversity within India surpassing levels observed in other global populations. Bayesian and non-Bayesian clustering analysis revealed low levels of genetic differentiation among sampled populations, except for the Southern Indian population. Demographic analysis using both mtDNA and microsatellites revealed that golden jackals in India have not experienced significant bottlenecks, while estimates of past effective population size suggested declines during the last 2500 generations, which corresponds to 7500-10 000 Ybp. Global phylogeographic analysis highlighted the distinctiveness of Indian jackals compared to other populations from across the species' distribution, with the highest number of haplotypes observed in Indian populations and no shared haplotypes observed between India and Middle Eastern or Indian and European populations. These findings are indicative of a long evolutionary history and bring new insights to inform targeted conservation management strategies for golden jackals, both locally and globally.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276768","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-level assembly of the serpentine endemic columbine, Aquilegia eximia". 特有的蛇形耧菜，Aquilegia eximia的近染色体水平组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-10 DOI: 10.1093/jhered/esaf035

Jason Johns, Merly Escalona, Courtney Miller, Noravit Chumchim, Oanh Nguyen, Mohan P A Marimuthu, Samuel Sacco, Colin Fairbairn, Eric Beraut, Erin Toffelmier, H Bradley Shaffer, Scott Hodges

{"title":"\"A near chromosome-level assembly of the serpentine endemic columbine, Aquilegia eximia\".","authors":"Jason Johns, Merly Escalona, Courtney Miller, Noravit Chumchim, Oanh Nguyen, Mohan P A Marimuthu, Samuel Sacco, Colin Fairbairn, Eric Beraut, Erin Toffelmier, H Bradley Shaffer, Scott Hodges","doi":"10.1093/jhered/esaf035","DOIUrl":"https://doi.org/10.1093/jhered/esaf035","url":null,"abstract":"The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, and especially in California. Here we report a near chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to two columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea 'Goldsmith'. The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably we found evidence that A. eximia, A. coerulea 'Goldsmith' and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259338","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

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Notholirion (Liliaceae). 山地隆升和气候振荡对百合科野百合属植物系统地理和物种分化的影响。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-04 DOI: 10.1093/jhered/esaf032

Rui-Yu Cheng, Juan Li, Deng-Feng Xie, Xing-Jin He, Ren-Xiu Zhou, Qing Li, Yanglina Yu, Song-Dong Zhou

{"title":"Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Notholirion (Liliaceae).","authors":"Rui-Yu Cheng, Juan Li, Deng-Feng Xie, Xing-Jin He, Ren-Xiu Zhou, Qing Li, Yanglina Yu, Song-Dong Zhou","doi":"10.1093/jhered/esaf032","DOIUrl":"https://doi.org/10.1093/jhered/esaf032","url":null,"abstract":"Investigating geological and climatic shifts in the Himalaya-Hengduan Mountains (HHM) and Qinghai-Tibet Plateau (QTP) is vital for unraveling environmental impacts on biogeography and evolution. We analyzed the evolutionary history of three Notholirion species across these regions, studying 254 individuals from 31 populations using 5 chloroplast DNA markers (matK, ndhA, ndhG-ndhI, petB-petD, and petL-petG) and nuclear ITS. A total of 1,145 low-copy nuclear genes (LCGs) and 112 chloroplast genes from 11 representative individuals were further utilized for phylogenetic reconstruction. Divergence timing was estimated with 147 plastomes, including 10 Notholirion populations. 14 cpDNA and 27 ITS haplotypes revealed species-specific variation. Phylogenetic analyses confirmed a monophyletic origin for all three species, with population-level nested relationships and cytonuclear discordance attributed to incomplete lineage sorting (ILS) and hybridization. Dating and ancestral reconstruction traced Notholirion's origin to the southern Himalayas during the Late Oligocene (25.05 Ma), with diversification commencing in the Late Pliocene (7.43 Ma). MaxEnt modeling indicated stable species distributions from the Last Interglacial to future projections. The initial split of Notholirion was triggered by climate changes following the uplift of the QTP. Subsequently, dramatic climatic fluctuations during the Pleistocene and the complex topography of the HHM region jointly promoted species dispersal and diversification, ultimately shaping its current biogeographic distribution and phylogenetic structure. High genetic diversity likely stems from prolonged evolutionary history, sexual reproduction, and habitat fragmentation. The high genetic differentiation observed among Notholirion populations may be attributed to pronounced environmental changes across their distribution range, along with limited seed production and dispersal capacity.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227730","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

Frequencies of house fly proto-Y chromosomes across populations are predicted by temperature heterogeneity within populations. 家蝇原 Y 染色体在不同种群中的频率是由种群内的温度异质性预测的。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-02 DOI: 10.1093/jhered/esae056

Patrick D Foy, Sara R Loetzerich, David Boxler, Edwin R Burgess, R T Trout Fryxell, Alec C Gerry, Nancy C Hinkle, Erika T Machtinger, Cassandra Olds, Aaron M Tarone, Wes Watson, Jeffrey G Scott, Richard P Meisel

{"title":"Frequencies of house fly proto-Y chromosomes across populations are predicted by temperature heterogeneity within populations.","authors":"Patrick D Foy, Sara R Loetzerich, David Boxler, Edwin R Burgess, R T Trout Fryxell, Alec C Gerry, Nancy C Hinkle, Erika T Machtinger, Cassandra Olds, Aaron M Tarone, Wes Watson, Jeffrey G Scott, Richard P Meisel","doi":"10.1093/jhered/esae056","DOIUrl":"10.1093/jhered/esae056","url":null,"abstract":"Sex chromosomes often differ between closely related species and can even be polymorphic within populations. Species with multifactorial sex determination segregate for multiple different sex-determining loci within populations, making them uniquely informative of the selection pressures that drive the evolution of sex chromosomes. The house fly (Musca domestica) is a model species for studying multifactorial sex determination because male-determining genes have been identified on all six of the chromosomes, which means that any chromosome can be a \"proto-Y.\" Natural populations of house flies also segregate for a recently derived female-determining locus, meaning house flies also have a proto-W chromosome. The different proto-Y chromosomes are distributed along latitudinal clines on multiple continents, their distributions can be explained by seasonality in temperature, and they have temperature-dependent effects on physiological and behavioral traits. It is not clear, however, how the clinal distributions interact with the effect of seasonality on the frequencies of house fly proto-Y and proto-W chromosomes across populations. To address this question, we measured the frequencies of house fly proto-Y and proto-W chromosomes across nine populations in the United States of America. We confirmed the clinal distribution along the eastern coast of North America, but it is limited to the eastern coast. In contrast, the annual mean daily temperature range predicts proto-Y chromosome frequencies across the entire continent. Our results therefore suggest that temperature heterogeneity can explain the distributions of house fly proto-Y chromosomes in a way that does not depend on the cline.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"208-215"},"PeriodicalIF":3.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481271","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

Whole-genome assembly and annotation of the firecracker penstemon (Penstemon eatonii). 爆竹草（Penstemon eatonii）的全基因组组装和注释。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-02 DOI: 10.1093/jhered/esae058

David E Jarvis, Mikel R Stevens, Payton Carter, Ying Fei Lin, Kate E Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B Stephensen, Hayley Mangelson, Noah H Williams, Carolyn A Wessinger, Peter J Maughan, Paul B Frandsen

{"title":"Whole-genome assembly and annotation of the firecracker penstemon (Penstemon eatonii).","authors":"David E Jarvis, Mikel R Stevens, Payton Carter, Ying Fei Lin, Kate E Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B Stephensen, Hayley Mangelson, Noah H Williams, Carolyn A Wessinger, Peter J Maughan, Paul B Frandsen","doi":"10.1093/jhered/esae058","DOIUrl":"10.1093/jhered/esae058","url":null,"abstract":"The penstemons are ornamental annual flowering plants native to the Intermountain West and Rocky Mountains and commonly used for urban landscaping. Elite commercial penstemons are generally susceptible to abiotic stresses, including drought, root rot, cold, and high salinity. Firecracker penstemon (Penstemon eatonii), however, is much more tolerant to these stresses than most elite cultivars. Importantly, firecracker penstemon has been reported to hybridize with many other penstemons and therefore provides the opportunity to develop more tolerant elite cultivars through strategic crossing. To facilitate the study and utilization of firecracker penstemon, we sequenced and annotated the genome of a P. eatonii accession collected from Utah, United States. We also performed low-coverage whole-genome sequencing of 26 additional accessions from three different varieties of P. eatonii. This chromosome-scale genome assembly is the most contiguous and complete Penstemon genome sequenced to date.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"373-381"},"PeriodicalIF":3.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12130433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513205","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

Secrets of the Goo: The genome assembly of the Pacific banana slug, Ariolimax columbianus. 粘的秘密：太平洋香蕉蛞蝓，Ariolimax columbianus的基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-02 DOI: 10.1093/jhered/esaf002

Maximilian Genetti, Merly Escalona, Cade Mirchandani, Jonas Oppenheimer, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Russell Corbett-Detig

{"title":"Secrets of the Goo: The genome assembly of the Pacific banana slug, Ariolimax columbianus.","authors":"Maximilian Genetti, Merly Escalona, Cade Mirchandani, Jonas Oppenheimer, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Russell Corbett-Detig","doi":"10.1093/jhered/esaf002","DOIUrl":"10.1093/jhered/esaf002","url":null,"abstract":"The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout the coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse. The evolutionary history, recent population history and environmental conditions leading to their phenotypic and genetic variation are not understood. To facilitate such research, we present the first high-quality de novo genome assembly of A. columbianus as part of the California Conservation Genomics Project. Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard California Conservation Genomics Project genome assembly protocol. This assembly comprises 401 scaffolds spanning 2.29 Gb, represented by a scaffold N50 of 94.9 Mb, a contig N50 of 3.7 Mb, and a benchmarking universal single-copy ortholog completeness score of 93.9%. Future work will use the A. columbianus genome to study the population structure of Ariolimax spp. across California to understand patterns of population structure, genetic diversity, and the broader ecological connections with their habitat. This data will contribute to the California Conservation Genomics Project, expanding the knowledge about the partitioning of genomic variation across the different ecoregions of California.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"335-343"},"PeriodicalIF":3.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12130430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030353","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

A chromosome-level reference genome for the common bed bug, Cimex lectularius, with identification of sex chromosomes. 普通臭虫（Cimex lectularius）的染色体级参考基因组，以及性染色体的鉴定。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-02 DOI: 10.1093/jhered/esae071

Lindsay S Miles, Richard Adams, Yannick Z Francioli, Daren C Card, Todd A Castoe, Warren Booth

{"title":"A chromosome-level reference genome for the common bed bug, Cimex lectularius, with identification of sex chromosomes.","authors":"Lindsay S Miles, Richard Adams, Yannick Z Francioli, Daren C Card, Todd A Castoe, Warren Booth","doi":"10.1093/jhered/esae071","DOIUrl":"10.1093/jhered/esae071","url":null,"abstract":"The common bed bug, Cimex lectularius, is a globally distributed pest insect of medical, veterinary, and economic importance. Previous reference genome assemblies for this species were generated from short-read sequencing data, resulting in a ~650 Mb composed of thousands of contigs. Here, we present a haplotype-resolved, chromosome-level reference genome, generated from an adult Harlen strain female specimen. Using PacBio long read and Omni-C proximity sequencing, we generated a 540 Mb genome with 15 chromosomes (13 autosomes and 2 sex chromosomes-X1X2) with an N50 > 30 Mb and BUSCO > 90%. Previous karyotyping efforts indicate an XY sex chromosome system, with 2n = 26 and X1X1X2X2 females and X1X2Y males; however, significant fragmentation of the X chromosome has also been reported. We further use whole genome resequencing data from males and females to identify the X1 and X2 chromosomes based on sex biases in coverage. This highly contiguous reference genome assembly provides a much-improved resource for identifying chromosomal genome architecture, and for interpreting patterns of urban outbreaks and signatures of selection linked to insecticide resistance.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"382-388"},"PeriodicalIF":3.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741134","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

Maintaining breed integrity: Successful introgression of the SLICK1 allele into the Holstein breed. 保持品种完整性：将 SLICK1 等位基因成功引入荷斯坦品种。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-02 DOI: 10.1093/jhered/esae057

Gabriel A Zayas, Serdal Dikmen, Raluca G Mateescu, Peter J Hansen

{"title":"Maintaining breed integrity: Successful introgression of the SLICK1 allele into the Holstein breed.","authors":"Gabriel A Zayas, Serdal Dikmen, Raluca G Mateescu, Peter J Hansen","doi":"10.1093/jhered/esae057","DOIUrl":"10.1093/jhered/esae057","url":null,"abstract":"This study evaluated the effectiveness of genetic introgression of the SLICK1 allele derived from Senepol cattle into the Holstein breed to enhance thermotolerance. The SLICK1 allele, located in the PRLR gene, confers a short and sleek coat that is inherited as a simple dominant phenotype. Approximately 40 years ago, the University of Florida initiated efforts to introgress this allele into the Holstein population. Here we tracked the introgression of the SLICK1 allele using a medium-density genotyping array and a reference population of both breeds (50 Holstein, 46 Senepol). Among the 31 SLICK1+ Holsteins, there was 15.25% ± 11.11% (mean ± SD) Senepol ancestry on BTA20. Holsteins at the University of Florida descended from slick matings that did not inherit the SLICK1 allele (n = 9) exhibited no Senepol ancestry. A secondary introgression of Senepol genetics in SLICK1+ animals was found on BTA4, spanning 54 markers and 15 genes, with 26.67% Senepol ancestry. This region, previously linked to heat stress adaptation, suggests that the introgression extends beyond the SLICK1 allele to incorporate additional beneficial genetics for thermal stress adaptation. These findings indicate that deliberate introgression of the SLICK1 allele enhances specific traits and potentially introduces other adaptive genetic variations. The study demonstrates the successful use of genetic interventions to improve livestock resilience against environmental challenges without significantly disrupting the recipient breed's genetic structure. The introgression of the SLICK1 allele serves as a model for breeding programs aimed at optimizing animal welfare and productivity in the face of global climate change while maintaining breed integrity.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"216-224"},"PeriodicalIF":3.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481272","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