Journal of Heredity最新文献_第8页

The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species. 孤岛橡树（Quercus tomentella）--一种孑遗的岛屿树种--的基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-03-13 DOI: 10.1093/jhered/esae002

Alayna Mead, Sorel T Fitz-Gibbon, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork

{"title":"The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species.","authors":"Alayna Mead, Sorel T Fitz-Gibbon, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork","doi":"10.1093/jhered/esae002","DOIUrl":"10.1093/jhered/esae002","url":null,"abstract":"Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit from information about its range-wide genetic structure and evolutionary history. Here we present a high-quality genome assembly for Q. tomentella, assembled using PacBio HiFi and Omni-C sequencing, developed as part of the California Conservation Genomics Project (CCGP). The resulting assembly has a length of 781 Mb, with a contig N50 of 22.0 Mb and a scaffold N50 of 63.4 Mb. This genome assembly will provide a resource for genomics-informed conservation of this rare oak species. Additionally, this reference genome will be the first one available for a species in Quercus section Protobalanus, a unique oak clade present only in western North America.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10936553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139673713","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

Lion Localizer: A software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA. Lion Localizer:一个软件工具，用于推断狮子(Panthera leo)的来源，使用线粒体DNA。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-03-13 DOI: 10.1093/jhered/esad072

Wesley C Au, Simon G Dures, Yasuko Ishida, Cory E Green, Kai Zhao, Rob Ogden, Alfred L Roca

{"title":"Lion Localizer: A software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA.","authors":"Wesley C Au, Simon G Dures, Yasuko Ishida, Cory E Green, Kai Zhao, Rob Ogden, Alfred L Roca","doi":"10.1093/jhered/esad072","DOIUrl":"10.1093/jhered/esad072","url":null,"abstract":"The illegal poaching of lions for their body parts poses a severe threat to lion populations across Africa. Poaching accounts for 35% of all human-caused lion deaths, with 51% attributed to retaliatory killings following livestock predation. In nearly half of the retaliatory killings, lion body parts are removed, suggesting that high demand for lion body parts may fuel killings attributed to human-lion conflict. Trafficked items are often confiscated in transit or destination countries far from their country of origin. DNA from lion parts may in some cases be the only available means for examining their geographic origins. In this paper, we present the Lion Localizer, a full-stack software tool that houses a comprehensive database of lion mitochondrial DNA (mtDNA) sequences sourced from previously published studies. The database covers 146 localities from across the African continent and India, providing information on the potential provenance of seized lion body parts. Lion mtDNA sequences of 350 or 1,140 bp corresponding to the cytochrome b region can be generated from lion products and queried against the Lion Localizer database. Using the query sequence, the Lion Localizer generates a listing of exact or partial matches, which are displayed on an interactive map of Africa. This allows for the rapid identification of potential regions and localities where lions have been or are presently being targeted by poachers. By examining the potential provenance of lion samples, the Lion Localizer serves as a valuable resource in the fight against lion poaching. The software is available at https://lionlocalizer.org.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89720628","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 of the wood stork (Mycteria americana) provides insight into avian chromosome evolution. 木鹳（Mycteria americana）的染色体级基因组为鸟类染色体进化提供了启示。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-03-13 DOI: 10.1093/jhered/esad077

Richard Flamio, Kristina M Ramstad

{"title":"Chromosome-level genome of the wood stork (Mycteria americana) provides insight into avian chromosome evolution.","authors":"Richard Flamio, Kristina M Ramstad","doi":"10.1093/jhered/esad077","DOIUrl":"10.1093/jhered/esad077","url":null,"abstract":"Despite being quite specious (~10,000 extant species), birds have a fairly uniform genome size and karyotype (including the common occurrence of microchromosomes) relative to other vertebrate lineages. Storks (Family Ciconiidae) are a charismatic and distinct group of large wading birds with nearly worldwide distribution but few genomic resources. Here we present an annotated chromosome-level reference genome and chromosome orthology analysis for the wood stork (Mycteria americana), a species that has been federally protected under the Endangered Species Act since 1984. The annotated chromosome-level reference assembly was produced using the blood of a wild female wood stork chick, has a length of 1.35 Gb, a contig N50 of 37 Mb, a scaffold N50 of 80 Mb, and a BUSCO score of 98.8%. We identified 31 autosomal pairs and two sex chromosomes in the wood stork genome, but failed to identify four additional autosomal microchromosomes previously found via karyotyping. Orthology analyses confirmed reported synapomorphies unique to storks and identified the chromosomes participating in these fusions. This study highlights the difficulty and potential problems associated with delineating microchromosomes in reference genome assemblies. It also provides a foundation for studying karyotype evolution in the core water bird clade that includes penguins, albatrosses, storks, cormorants, herons, and ibises. Finally, our reference genome will allow for numerous genomic studies, such as genome-wide association studies of local adaptation, that will aid in wood stork conservation.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138813204","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

Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction. 基因组分析表明，开普狮子种群在殖民地灭绝前具有连通性。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-03-13 DOI: 10.1093/jhered/esad081

Alida de Flamingh, Thomas P Gnoske, Angel G Rivera-Colón, Velizar A Simeonovski, Julian C Kerbis Peterhans, Nobuyuki Yamaguchi, Kelsey E Witt, Julian Catchen, Alfred L Roca, Ripan Singh Malhi

{"title":"Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction.","authors":"Alida de Flamingh, Thomas P Gnoske, Angel G Rivera-Colón, Velizar A Simeonovski, Julian C Kerbis Peterhans, Nobuyuki Yamaguchi, Kelsey E Witt, Julian Catchen, Alfred L Roca, Ripan Singh Malhi","doi":"10.1093/jhered/esad081","DOIUrl":"10.1093/jhered/esad081","url":null,"abstract":"Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the \"Cape Flats\" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as \"black-maned lions\" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139049803","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

Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera. 漂移驱动染色体数目的进化 I：性状转变对鞘翅目昆虫基因组进化的影响。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-03-13 DOI: 10.1093/jhered/esae001

Heath Blackmon, Michelle M Jonika, James M Alfieri, Leen Fardoun, Jeffery P Demuth

{"title":"Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera.","authors":"Heath Blackmon, Michelle M Jonika, James M Alfieri, Leen Fardoun, Jeffery P Demuth","doi":"10.1093/jhered/esae001","DOIUrl":"10.1093/jhered/esae001","url":null,"abstract":"Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an important role to chromosomal mutations. When the effective population size (Ne) is small, the efficacy of selection is weakened, and the likelihood of fixing underdominant mutations by genetic drift is greater. Thus, it is possible that ecological and phenotypic transitions that modulate Ne facilitate the fixation of chromosome changes, increasing the rate of karyotype evolution. We synthesize all available chromosome number data in Coleoptera and estimate the impact of traits expected to change Ne on the rate of karyotype evolution in the family Carabidae and 12 disparate clades from across Coleoptera. Our analysis indicates that in Carabidae, wingless clades have faster rates of chromosome number increase. Additionally, our analysis indicates clades exhibiting multiple traits expected to reduce Ne, including strict inbreeding, oligophagy, winglessness, and island endemism, have high rates of karyotype evolution. Our results suggest that chromosome number changes are likely fixed by genetic drift despite an initial fitness cost and that chromosomal speciation models may be important to consider in clades with very small Ne.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10936555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139106930","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

Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea). 北美西部爬行动物多样化的重复模式得到了北方鳄蜥(Elgaria coerulea)的支持。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad073

Adam D Leaché, Hayden R Davis, Chris R Feldman, Matthew K Fujita, Sonal Singhal

{"title":"Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea).","authors":"Adam D Leaché, Hayden R Davis, Chris R Feldman, Matthew K Fujita, Sonal Singhal","doi":"10.1093/jhered/esad073","DOIUrl":"10.1093/jhered/esad073","url":null,"abstract":"Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10838131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138048837","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 insights into isolation of the threatened Florida crested caracara (Caracara plancus). 对受威胁的佛罗里达冠卡拉（caracara plancus）分离的基因组见解。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad057

Natalie Payne, John A Erwin, Joan L Morrison, James F Dwyer, Melanie Culver

{"title":"Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus).","authors":"Natalie Payne, John A Erwin, Joan L Morrison, James F Dwyer, Melanie Culver","doi":"10.1093/jhered/esad057","DOIUrl":"10.1093/jhered/esad057","url":null,"abstract":"We conducted a population genomic study of the crested caracara (Caracara plancus) using samples (n = 290) collected from individuals in Florida, Texas, and Arizona, United States. Crested caracaras are non-migratory raptors ranging from the southern tip of South America to the southern United States, including a federally protected relict population in Florida long thought to have been isolated since the last ice age. Our objectives were to evaluate genetic diversity and population structure of Florida's apparently isolated population and to evaluate taxonomic relationships of crested caracaras at the northern edge of their range. Using DNA purified from blood samples, we conducted double-digest restriction site associated DNA sequencing and sequenced the mitochondrial ND2 gene. Analyses of population structure using over 9,000 SNPs suggest that two major clusters are best supported, one cluster including only Florida individuals and the other cluster including Arizona and Texas individuals. Both SNPs and mitochondrial haplotypes reveal the Florida population to be highly differentiated genetically from Arizona and Texas populations, whereas, Arizona and Texas populations are moderately differentiated from each other. The Florida population's mitochondrial haplotypes form a separate monophyletic group, while Arizona and Texas populations share mitochondrial haplotypes. Results of this study provide substantial genetic evidence that Florida's crested caracaras have experienced long-term isolation from caracaras in Arizona and Texas and thus, represent a distinct evolutionary lineage possibly warranting distinction as an Evolutionarily Significant Unit (ESU) or subspecies. This study will inform conservation strategies focused on long-term survival of Florida's distinct, panmictic population.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220447","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

Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer's Pochard (Aythya baeri) in North America. 使用PMx将经验亲属关系整合到迁地人口管理中的方法学意义：北美Baer’s Pochard（Aythya baeri）的案例研究。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad069

Asako Y Chaille, Robert C Lacy, Andrea S Putnam, Jamie L Toste, Aryn P Wilder, Jamie A Ivy

{"title":"Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer's Pochard (Aythya baeri) in North America.","authors":"Asako Y Chaille, Robert C Lacy, Andrea S Putnam, Jamie L Toste, Aryn P Wilder, Jamie A Ivy","doi":"10.1093/jhered/esad069","DOIUrl":"10.1093/jhered/esad069","url":null,"abstract":"The application of molecular tools to population management can improve the long-term genetic viability of ex situ populations. In this study, we aimed to understand the implications of integrating empirical kinships into the genetic management of an ex situ population of the endangered waterfowl, Baer's pochard (Aythya baeri), in North America. Single nucleotide polymorphism data were generated for 141 Baer's pochard using double digest restriction site-associated DNA sequencing and empirical kinships were derived and integrated into the population management software PMx. Analyses suggested 37.7% of pairwise relationships previously assumed to be unrelated were first, second, or third-order relatives. We determined that most genetic summary statistics were impacted through the calculation of the population's mean kinship, which increased from MK¯=0.0772 to MK¯=0.2074 after empirical kinships were integrated into our analyses. Our results also revealed the importance of understanding how molecular kinships derived from a particular estimator are scaled, if the scale differs significantly from pedigree-based kinships. We describe the theory behind the genetic metrics impacted and provide general guidance on incorporating empirical kinships into ex situ population management as well as provide suggestions for sampling strategies to minimize the biases inherent in merging two types of kinship estimators.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71489123","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 reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides. 向日葵海星的生态修复参考基因组。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad054

Lauren M Schiebelhut, Melissa B DeBiasse, Lars Gabriel, Katharina J Hoff, Michael N Dawson

{"title":"A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides.","authors":"Lauren M Schiebelhut, Melissa B DeBiasse, Lars Gabriel, Katharina J Hoff, Michael N Dawson","doi":"10.1093/jhered/esad054","DOIUrl":"10.1093/jhered/esad054","url":null,"abstract":"Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses-as well as their integration across scales-of SSW and environmental stressors.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10838127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41167083","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 highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris. 一个高度连续的口袋鼠长颚鼠基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad060

Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman

{"title":"A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.","authors":"Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman","doi":"10.1093/jhered/esad060","DOIUrl":"10.1093/jhered/esad060","url":null,"abstract":"The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10838119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41174001","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