Journal of Heredity最新文献_第7页

A genome assembly for Lahontan Cutthroat Trout, Oncorhynchus clarkii henshawi. 拉洪塘切喉鳟鱼的基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-11 DOI: 10.1093/jhered/esaf050

Cheyenne Y Payne, Merly Escalona, Shannon R Kieran Blair, Amanda J Finger, Richard E Green, Devon Pearse, Jeff Rodzen, John Carlos Garza

引用次数: 0

A Chromosome-Level Genome Assembly of the Snow Leopard, Panthera Uncia. 雪豹（Panthera Uncia）染色体水平基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-09 DOI: 10.1093/jhered/esaf046

Plasil Martin, Winter Sven, Stejskalova Karla, Vychodilova Leona, Jelinek April, Futas Jan, Burger A Pamela, Horin Petr

{"title":"A Chromosome-Level Genome Assembly of the Snow Leopard, Panthera Uncia.","authors":"Plasil Martin, Winter Sven, Stejskalova Karla, Vychodilova Leona, Jelinek April, Futas Jan, Burger A Pamela, Horin Petr","doi":"10.1093/jhered/esaf046","DOIUrl":"https://doi.org/10.1093/jhered/esaf046","url":null,"abstract":"The snow leopard (Panthera uncia), a vulnerable big cat native to Central Asia, faces an ongoing population decline due to habitat loss and human activities. Despite its conservation importance, genomic resources for this species remain limited. High-quality reference genomes are essential for assessing genetic diversity, structural variation, and evolutionary history. To address this gap, we have generated a long-read-based and proximity-ligation scaffolded de novo genome assembly of a male snow leopard. The final assembly has a total length of 2.46 Gb in 280 scaffolds, of which the 19 largest correspond to the 18 autosomes and the X chromosome. The scaffold N50 is 145.76 Mb, and the L50 is seven scaffolds. BUSCO and compleasm scores are 98.7% and 98.9% of identified Carnivora orthologs. Telomeric sequences were identified on at least one end of 18 out of 19 chromosomes. Scaffolds corresponding to the Y chromosome were identified and mapped. Additionally, the assembly's annotation identified a repeat content of 42.27% and 25 391 genes. We produced a high-quality, long-read-based chromosome-level assembly of a male snow leopard, as evidenced by the data above. As a first assembly of a male genome, it can serve as a suitable reference genome for the species. The Y chromosome scaffolds provide a glimpse into the chromosome organization and interspecies differences.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592966","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

Correction to: Pervasive genomic signatures of local adaptation to altitude across highland specialist Andean hummingbird populations. 更正：普遍的基因组特征在高原专家安第斯蜂鸟种群对当地海拔的适应。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-08 DOI: 10.1093/jhered/esaf044

引用次数: 0

A genome assembly for a textbook mammalian study species, the California ground squirrel (Otospermophilus beecheyi). 一个教科书哺乳动物研究物种的基因组组装，加利福尼亚地松鼠（otospermoophilus beecheyi）。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-02 DOI: 10.1093/jhered/esaf045

Matthew L Holding, Sree Rohit Raj Kolora, Jennifer E Smith, Shana L McDevitt, Peter H Sudmant, Rebecca D Tarvin

{"title":"A genome assembly for a textbook mammalian study species, the California ground squirrel (Otospermophilus beecheyi).","authors":"Matthew L Holding, Sree Rohit Raj Kolora, Jennifer E Smith, Shana L McDevitt, Peter H Sudmant, Rebecca D Tarvin","doi":"10.1093/jhered/esaf045","DOIUrl":"https://doi.org/10.1093/jhered/esaf045","url":null,"abstract":"Squirrels (Rodentia; Sciuridae) are a well-known and diverse group of rodents, including the charismatic ground-dwelling members of the Tribe Marmotini. In particular, the California ground squirrel (Otospermophilus beecheyi) is an emerging model system for the study of social and risk-sensitive behaviors in a rapidly changing world, as well as the physiology of resistance to snake venoms. To complement extensive natural history information for O. beecheyi, we provide a chromosome-scale genome to facilitate molecular studies focused on the genetic basis of ecologically important traits, population genetics, comparative genomics, and social evolution. The final scaffolded genome was 2.27 Gb contained in 9960 contigs and placed into 1383 scaffolds. The scaffold N50 was just over 125 Mb. We used the presence of 10 248 complete genes detected by BUSCO v5 specifically to compare broad patterns of chromosomal synteny between chromosomal scaffolds for O. beecheyi and two other sciurid rodents. The recovered pattern of synteny suggests several fusion and fission events for O. beecheyi in relation to the other two species. Taken together, this new information should advance our understanding of O. beecheyi and comparative studies of mammalian genomic biology and evolution.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546229","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

Near-Gapless Genome Assemblies of the Domestic Cat (Felis silvestris catus) and the African Serval (Leptailurus serval) Derived from Trio-Binning. 来自Trio-Binning的家猫（Felis silvestris catus）和非洲几种猫（Leptailurus Serval）的近无间隙基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-02 DOI: 10.1093/jhered/esaf047

Andrew J Harris, Terje Raudsepp, Nicole M Foley, Wesley C Warren, Leslie A Lyons, William J Murphy

{"title":"Near-Gapless Genome Assemblies of the Domestic Cat (Felis silvestris catus) and the African Serval (Leptailurus serval) Derived from Trio-Binning.","authors":"Andrew J Harris, Terje Raudsepp, Nicole M Foley, Wesley C Warren, Leslie A Lyons, William J Murphy","doi":"10.1093/jhered/esaf047","DOIUrl":"https://doi.org/10.1093/jhered/esaf047","url":null,"abstract":"The Savannah cat is a popular cat breed derived from an interspecific hybrid cross between the domestic cat (Felis silvestris catus) and the African serval (Leptailurus serval). Within the family Felidae, Savannahs represent the most divergent interspecific hybrid breed, with ~13 million years separating the parental species. Here, we apply trio-binning of an F1 interspecific hybrid to achieve near-gapless chromosome-level genome assemblies for the domestic cat and serval. Using a hybrid assembly approach combining PacBio HiFi and CLR reads, we generated domestic cat and serval genome assemblies, each comprising ~2.5 Gb of sequence with contig N50s of 107.4Mb and 112.3Mb, respectively. We anchored >99% of the contigs into 19 chromosome-length scaffolds for each species, supported by base-quality (QV) metrics exceeding 61. The serval reference genome assembly represents the first for the species, providing an essential resource for future population and comparative genomic studies. The new domestic cat assembly adds an average of 36-Mb of novel sequence to chromosomes missing in earlier long-read assemblies. These sequence gains include the first resolution of multi-megabase FA-SAT macrosatellite arrays with putative functions in cell cycle regulation. These new assemblies add to the growing list of highly complete chromosome-level felid genomes and improve our understanding of complex genome architecture and satellite evolution within mammals.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546231","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

Small snakes, big cities: population genetics of urban Dekay's brown snake (Storeria dekayi) in New Jersey. 小蛇，大城市：新泽西州城市德凯褐蛇（Storeria dekayi）的种群遗传学。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-25 DOI: 10.1093/jhered/esaf042

Tianqi Huang, Isaac Overcast, Arianna Kuhn, Peter J Morin, Sara Ruane

{"title":"Small snakes, big cities: population genetics of urban Dekay's brown snake (Storeria dekayi) in New Jersey.","authors":"Tianqi Huang, Isaac Overcast, Arianna Kuhn, Peter J Morin, Sara Ruane","doi":"10.1093/jhered/esaf042","DOIUrl":"https://doi.org/10.1093/jhered/esaf042","url":null,"abstract":"Despite the unprecedented rate of global urbanization, a diverse array of taxa are supported in urban areas. However, the long-term persistence of urban wildlife cannot be guaranteed due to the various adverse effects that come with urbanization, such as resource depletion and reduced gene flow. Accordingly, it is imperative to evaluate the health and viability of urban wildlife, particularly of species that are underrepresented in the existing literature, like herpetofauna. Genomic techniques can provide critical insights into urban wildlife health and population viability. Here, we generated a ddRADseq dataset of 162 Dekay's brown snakes (Storeria dekayi) among 11 locations with different urbanization magnitudes across New Jersey, USA, and examined the population genetic patterns of this common urban reptile. While genetic diversity was not severely reduced within those populations, we uncovered the presence of genetic differentiation and structuring across them, especially for those from the most urbanized areas. Deviations of interpopulation structure from their geographic distributions might reflect either habitat alteration or human intervention in recent history. Landscape genetic analyses revealed the presence of an isolation-by-distance relationship that was only significant within a short spatial distance of 1500 m. Most urban populations also displayed lower-than-expected historic migration and diversity rates, but some remained genetically connected and diverse. To conclude, our study can serve as a useful guide for population genomic studies on urban herpetofauna. Based on our results, urbanization is likely to impact interpopulation genetic connectivity, but to have limited effects on intrapopulation genetic diversity of small-bodied, terrestrial urban dwellers.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487155","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 reference genome assembly for Gilbert's skink Plestiodon gilberti. 吉尔伯特氏石龙Plestiodon gilberti的染色体水平参考基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-23 DOI: 10.1093/jhered/esaf040

Jonathan Q Richmond, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Benjamin R Karin, Robert D Cooper, Robert N Fisher, Ian J Wang, H Bradley Shaffer

{"title":"A chromosome-level reference genome assembly for Gilbert's skink Plestiodon gilberti.","authors":"Jonathan Q Richmond, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Benjamin R Karin, Robert D Cooper, Robert N Fisher, Ian J Wang, H Bradley Shaffer","doi":"10.1093/jhered/esaf040","DOIUrl":"https://doi.org/10.1093/jhered/esaf040","url":null,"abstract":"Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert's skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project (CCGP). This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. Although members of the Scincidae comprise nearly one-quarter of all lizard species (1785 described species), this de novo assembly represents one of only 10 skink species globally and the first North American skink with a reference genome. The assembly has a total length of ~ 1.57 Gb, a scaffold N50 length of ~ 231.32 Mb, read coverage of ~56X, and BUSCO completeness score of 97.2% based on the Tetrapoda ortholog database. Plestiodon gilberti is a member of the Plestiodon skiltonianus species complex, a group with many of the characteristics of ecological speciation but where ancient hybridization events present challenges to disentangling the initial patterns of lineage divergence. Combined with dense sampling of resequenced genomes in the CCGP, including other members of the P. skiltonianus complex, this reference genome will enable future analyses of the links between divergent selection and the genes underlying speciation, as well as the potential for introgression to enable adaptation to new or changing environments.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531180","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 hybrid de novo genome assembly of the digger wasp Cerceris sabulosa (Hymenoptera, Crabronidae). 土蜂（膜翅目，姬蜂科）的杂交基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-20 DOI: 10.1093/jhered/esaf041

Xiaoli Li, Ye Xiao, Qingsong Zhou, Mei Xiong, Xin Zhou

引用次数: 0

Demographic expansion and panmixia in a St. Martin Endemic, Anolis pogus, Coincides with the decline of a competitor. 圣马丁地方病Anolis pogus的人口扩张和panmixia，与竞争对手的衰落同时发生。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-06-17 DOI: 10.1093/jhered/esaf039

Michael L Yuan, Joost Merjenburgh, Timothy P Wagensveld, Lauren A Esposito, Rayna C Bell, Edward A Myers

{"title":"Demographic expansion and panmixia in a St. Martin Endemic, Anolis pogus, Coincides with the decline of a competitor.","authors":"Michael L Yuan, Joost Merjenburgh, Timothy P Wagensveld, Lauren A Esposito, Rayna C Bell, Edward A Myers","doi":"10.1093/jhered/esaf039","DOIUrl":"https://doi.org/10.1093/jhered/esaf039","url":null,"abstract":"Understanding patterns of differentiation at microgeographic scales can enhance our understanding of evolutionary dynamics and lead to the development of effective conservation strategies. In particular, high levels of landscape heterogeneity can strongly influence species abundances, genetic structure, and demographic trends. The bearded anole, Anolis pogus, is endemic to the topographically complex island of St. Martin and of conservation concern. Here, we examined genetic diversity and inbreeding, assessed which features of the landscape influence population abundances, tested for population genetic structure across St. Martin, and inferred historical demographic trends. We found minimal inbreeding or low genetic diversity in A. pogus. We found that suitable habitat occurs broadly across the island and that population abundances were largely predicted by canopy cover. However, there was no signature of population genetic structure across the distribution, in contrast to the co-distributed anole species (Anolis gingivinus). Historical demographic trends in A. pogus were in sharp contrast to A. gingivinus, with effective population sizes of A. pogus increasing in the recent past while A. gingivinus population sizes have declined. We posit that declines in a competitor species allowed for population size expansion in A. pogus. Overall, these analyses suggest that A. pogus is unlikely to be of immediate conservation concern. Further, we highlight the role of demographic history and ecological interactions in shaping population structure.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509494","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

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