Journal of Heredity最新文献_第6页

Large variance in inbreeding within the Iberian wolf population. 伊比利亚狼种群内近亲繁殖的差异很大。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad071

Isabel Salado, Michaela Preick, Natividad Lupiáñez-Corpas, Alberto Fernández-Gil, Carles Vilà, Michael Hofreiter, Jennifer A Leonard

{"title":"Large variance in inbreeding within the Iberian wolf population.","authors":"Isabel Salado, Michaela Preick, Natividad Lupiáñez-Corpas, Alberto Fernández-Gil, Carles Vilà, Michael Hofreiter, Jennifer A Leonard","doi":"10.1093/jhered/esad071","DOIUrl":"10.1093/jhered/esad071","url":null,"abstract":"The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300 to 350 packs and then stabilized. In contrast to many current European wolf populations, which have been connected through gene flow, the Iberian wolf population has been isolated for decades. Here, we measured changes in genomic diversity and inbreeding through the last decades in a geographic context. We find that the level of genomic diversity in Iberian wolves is low compared with other Eurasian wolf populations. Despite population expansion in the last 50 years, some modern wolves had very high inbreeding, especially in the recently recolonized and historical edge areas. These individuals contrast with others with low inbreeding within the same population. The high variance in inbreeding despite population expansion seems associated with small-scale fragmentation of the range that is revealed by the genetic similarity between modern and historical samples from close localities despite being separated by decades, remaining differentiated from other individuals that are just over 100 km away, a small distance for a species with great dispersal capacity inhabiting a continuous range. This illustrates that, despite its demographically stable condition, the population would probably benefit from favoring connectivity within the population as well as genetic exchange with other European wolf populations to avoid excessive fragmentation and local inbreeding depression.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11235127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89720627","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

The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity. 基因拯救下局部适应性的进化动态取决于突变负荷和多基因性。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad079

Yulin Zhang, Aaron J Stern, Rasmus Nielsen

{"title":"The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity.","authors":"Yulin Zhang, Aaron J Stern, Rasmus Nielsen","doi":"10.1093/jhered/esad079","DOIUrl":"10.1093/jhered/esad079","url":null,"abstract":"Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success of GR depends on several factors-such as their demographic history and distribution of dominance effects of mutations-that may vary across populations. While we understand the impact of these factors on the dynamics of GR, their impact on local adaptations remains unclear. To this end, we conduct a population genetics simulation study to evaluate the impact of trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history on the efficacy of GR. We find that the impact on local adaptations depends highly on the mutational load at the time of GR, which is in turn shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. Over time local adaptations are generally restored post-GR, though in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation affecting the trait is replaced by donor variation can vary drastically and is especially high for complex traits. Our results provide insights on the impact of GR on trait evolution and considerations for the practical implementation of GR.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11235128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139038218","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

Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs. 全基因组分析揭示了加拉帕戈斯铁轨鸟（鸟类：Rallidae）的多样化，并证实了山羊根除计划的成功。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-07-10 DOI: 10.1093/jhered/esae017

Daniel E Chavez, Taylor Hains, Sebastian Espinoza-Ulloa, Robert K Wayne, Jaime A Chaves

{"title":"Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs.","authors":"Daniel E Chavez, Taylor Hains, Sebastian Espinoza-Ulloa, Robert K Wayne, Jaime A Chaves","doi":"10.1093/jhered/esae017","DOIUrl":"10.1093/jhered/esae017","url":null,"abstract":"Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2 Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140159543","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

The difficulty of detecting inbreeding depression and its effect on conservation decisions. 检测近亲繁殖抑制的难度及其对保护决策的影响。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad080

Sarah R Hoy, Kristin E Brzeski, Leah M Vucetich, Rolf O Peterson, John A Vucetich

{"title":"The difficulty of detecting inbreeding depression and its effect on conservation decisions.","authors":"Sarah R Hoy, Kristin E Brzeski, Leah M Vucetich, Rolf O Peterson, John A Vucetich","doi":"10.1093/jhered/esad080","DOIUrl":"10.1093/jhered/esad080","url":null,"abstract":"Statistical inferences about inbreeding depression are often derived from analyses with low power and a high risk of failing to detect inbreeding depression. That risk is widely appreciated by scientists familiar with the relevant statistical and genetical theory, but may be overlooked and underappreciated by decision-makers. Consequently, there is value in demonstrating this risk using a real example. We use data from the wolf population on Isle Royale to demonstrate the difficulty of making reliable statistical inferences about inbreeding depression. This wolf population is known-by other methods-to have gone effectively extinct due to deleterious genetic processes associated with inbreeding. Beyond that demonstration, we use two case-studies-wolves on Isle Royale and vaquita (porpoises) from the Gulf of California, Mexico-to show how statistical inferences about inbreeding depression can affect conservation decisions. According to most decision theory, decisions depend importantly on: 1) probabilities that certain states exist (e.g. inbreeding depression is present) and 2) the utility assigned to various outcomes (e.g. the value of acting to mitigate inbreeding when it is present). The probabilities are provided by statistical inference; whereas utilities are almost entirely determined by normative values and judgements. Our analysis suggests that decisions to mitigate inbreeding depression are often driven more by utilities (normative values) than probabilities (statistical inferences). As such, advocates for mitigating inbreeding depression will benefit from better communicating to decision-makers the value of populations persisting and the extent to which decisions should depend on normative values.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138886562","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

Mutation of mpv17 results in loss of iridophores due to mitochondrial dysfunction in tilapia. mpv17 基因突变会导致罗非鱼线粒体功能障碍而失去虹膜。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-07-01 DOI: 10.1093/jhered/esae034

Jia Xu, Peng Li, Mengmeng Xu, Chenxu Wang, Thomas D Kocher, Deshou Wang

{"title":"Mutation of mpv17 results in loss of iridophores due to mitochondrial dysfunction in tilapia.","authors":"Jia Xu, Peng Li, Mengmeng Xu, Chenxu Wang, Thomas D Kocher, Deshou Wang","doi":"10.1093/jhered/esae034","DOIUrl":"https://doi.org/10.1093/jhered/esae034","url":null,"abstract":"Mpv17 (mitochondrial inner membrane protein MPV17) deficiency causes severe mitochondrial DNA depletion syndrome in mammals and loss of pigmentation of iridophores and a significant decrease of melanophores in zebrafish. The reasons for this are still unclear. In this study, we established an mpv17 homozygous mutant line in Nile tilapia. The developing mutants are transparent due to loss of iridophores and aggregation of pigment granules in the melanophores and disappearance of the vertical pigment bars on the side of the fish. Transcriptome analysis using skin of fish at 30 dpf (days post fertilization) revealed that the genes related to purine (especially pnp4a) and melanin synthesis were significantly downregulated. However, administration of guanine diets failed to rescue the phenotype of the mutants. In addition, no obvious apoptosis signals were observed in the iris of the mutants by TUNEL staining. Significant downregulation of genes related to iridophore differentiation was detected by qPCR. Insufficient ATP, as revealed by ATP assay, α-MSH treatment and adcy5 mutational analysis, might account for the defects of melanophores in mpv17 mutants. Several tissues displayed less mtDNA and decreased ATP levels. Taken together, these results indicated that mutation of mpv17 led to mitochondrial dTMP deficiency, followed by impaired mtDNA content and mitochondrial function, which in turn, led to loss of iridophores and a transparent body color in tilapia.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472787","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

The role of satellite DNAs in the chromosomal rearrangements and the evolution of the rare XY1Y2 sex system in Harttia (Siluriformes: Loricariidae). 卫星 DNA 在 Harttia（丝形目：萝栗科）染色体重排和罕见的 XY1Y2 性别系统进化中的作用。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-17 DOI: 10.1093/jhered/esae028

Geize Aparecida Deon, Rodrigo Zeni Dos Santos, Francisco de Menezes Cavalcante Sassi, Orlando Moreira-Filho, Marcelo Ricardo Vicari, Fábio Porto-Foresti, Ricardo Utsunomia, Marcelo de Bello Cioffi

{"title":"The role of satellite DNAs in the chromosomal rearrangements and the evolution of the rare XY1Y2 sex system in Harttia (Siluriformes: Loricariidae).","authors":"Geize Aparecida Deon, Rodrigo Zeni Dos Santos, Francisco de Menezes Cavalcante Sassi, Orlando Moreira-Filho, Marcelo Ricardo Vicari, Fábio Porto-Foresti, Ricardo Utsunomia, Marcelo de Bello Cioffi","doi":"10.1093/jhered/esae028","DOIUrl":"https://doi.org/10.1093/jhered/esae028","url":null,"abstract":"The underlying processes behind the formation, evolution, and long-term maintenance of multiple sex chromosomes have been largely neglected. Among vertebrates, fishes represent the group with the highest diversity of multiple sex chromosome systems and, with six instances, the Neotropical fish genus Harttia stands out by presenting the most remarkable diversity. However, although the origin mechanism of their sex chromosome systems is well discussed, little is known about the importance of some repetitive DNA classes in the differentiation of multiple systems. In this work, by employing a combination of cytogenetic and genomic procedures, we evaluated the satellite DNA composition of H. carvalhoi with a focus on their role in the evolution, structure, and differentiation process of the rare XY1Y2 multiple sex chromosome system. The genome of H. carvalhoi contains a total of 28 satellite DNA families, with the A+T content ranging between 38,1 and 68,1% and the predominant presence of long satellites. The in situ hybridization experiments detected 15 satellite DNAs with positive hybridization signals mainly on centromeric and pericentromeric regions of almost all chromosomes or clustered on a few pairs. Five of them presented clusters on X, Y1, and/or Y2 sex chromosomes which were therefore selected for comparative hybridization in the other three congeneric species. We found several conserved satellites accumulated on sex chromosomes and also in regions that were involved in chromosomal rearrangements. Our results provide a new contribution of satellitome studies in multiple sex chromosome systems in fishes and represent the first satellitome study for a Siluriformes species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960809","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

Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow). 微塑料暴露与模式生物黑头鲦鱼（Pimephales promelas）的表观基因组效应有关。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-14 DOI: 10.1093/jhered/esae027

Miranda J Wade, Kennedy Bucci, Chelsea M Rochman, Mariah H Meek

{"title":"Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow).","authors":"Miranda J Wade, Kennedy Bucci, Chelsea M Rochman, Mariah H Meek","doi":"10.1093/jhered/esae027","DOIUrl":"https://doi.org/10.1093/jhered/esae027","url":null,"abstract":"Microplastics have evolutionary and ecological impacts across species, affecting organisms' development, reproduction, and behavior along with contributing to genotoxicity and stress. As plastic pollution is increasing and ubiquitous, gaining a better understanding of organismal responses to microplastics is necessary. Epigenetic processes such as DNA methylation are heritable forms of molecular regulation influenced by environmental conditions. Therefore, determining such epigenetic responses to microplastics will reveal potential chronic consequences of this environmental pollutant. We performed an experiment across two generations of fathead minnows (Pimephales promelas) to elucidate transgenerational epigenetic effects of microplastic exposure. We exposed the first generation of fish to four different treatments of microplastics: two concentrations of each of pre-consumer polyethylene (PE) and PE collected from Lake Ontario. We then raised the first filial generation with no microplastic exposure. We used enzymatic methylation sequencing on adult liver tissue and homogenized larvae to evaluate DNA methylation differences among treatments, sexes, and generations. Our findings show the origin of the plastic had a larger effect in female minnows whereas the effect of concentration was stronger in the males. We also observed transgenerational effects, highlighting a mechanism in which parents can pass on the effects of microplastic exposure to their offspring. Many of the genes found within differentially methylated regions in our analyses are known to interact with estrogenic chemicals associated with plastic and are related to metabolism. This study highlights the persistent and potentially serious impacts of microplastic pollution on gene regulation in freshwater systems.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923715","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 highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). 黄莺（Setophaga petechia）高度连续的基因组组装。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae008

Whitney L E Tsai, Merly Escalona, Kimball L Garrett, Ryan S Terrill, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, William Seligmann, Colin W Fairbairn, Ryan J Harrigan, John E McCormack, Michael E Alfaro, Thomas B Smith, Rachael A Bay

引用次数: 0

Genomic data revealed inbreeding despite a geographically connected stable effective population size since the Holocene in the protected Formosan Long-Arm Scarab beetle, Cheirotonus formosanus. 基因组数据显示，尽管自全新世以来受保护的台湾长臂猩甲虫（Cheirotonus formosanus）的有效种群规模保持稳定，但仍存在地理上相互连接的近亲繁殖现象。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae006

Jen-Pan Huang, Shu-Ping Wu, Wei-Yun Chen, Guan Jie Pham, Yi-Hsiu Kuan

{"title":"Genomic data revealed inbreeding despite a geographically connected stable effective population size since the Holocene in the protected Formosan Long-Arm Scarab beetle, Cheirotonus formosanus.","authors":"Jen-Pan Huang, Shu-Ping Wu, Wei-Yun Chen, Guan Jie Pham, Yi-Hsiu Kuan","doi":"10.1093/jhered/esae006","DOIUrl":"10.1093/jhered/esae006","url":null,"abstract":"Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747778","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

Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases. 利用公共数据库中的长短线程序列改进南美白对虾的基因组组装。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae015

Ricardo Perez-Enriquez, Oscar E Juárez, Pavel Galindo-Torres, Ana Luisa Vargas-Aguilar, Raúl Llera-Herrera

{"title":"Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases.","authors":"Ricardo Perez-Enriquez, Oscar E Juárez, Pavel Galindo-Torres, Ana Luisa Vargas-Aguilar, Raúl Llera-Herrera","doi":"10.1093/jhered/esae015","DOIUrl":"10.1093/jhered/esae015","url":null,"abstract":"The Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei is a highly relevant species for the world's aquaculture development, for which an incomplete genome is available in public databases. In this work, PacBio long-reads from 14 publicly available genomic libraries (131.2 Gb) were mined to improve the reference genome assembly. The libraries were assembled, polished using Illumina short-reads, and scaffolded with P. vannamei, Feneropenaeus chinensis, and Penaeus monodon genomes. The reference-guided assembly, organized into 44 pseudo-chromosomes and 15,682 scaffolds, showed an improvement from previous reference genomes with a genome size of 2.055 Gb, N50 of 40.14 Mb, L50 of 21, and the longest scaffold of 65.79 Mb. Most orthologous genes (92.6%) of the Arthropoda_odb10 database were detected as \"complete,\" and BRAKER predicted 21,816 gene models; from these, we detected 1,814 single-copy orthologues conserved across the genomic references for Marsupenaeus japonicus, F. chinensis, and P. monodon. Transcriptomic-assembly data aligned in more than 99% to the new reference-guided assembly. The collinearity analysis of the assembled pseudo-chromosomes against the P. vannamei and P. monodon reference genomes showed high conservation in different sets of pseudo-chromosomes. In addition, more than 21,000 publicly available genetic marker sequences were mapped to single-site positions. This new assembly represents a step forward to previously reported P. vannamei assemblies. It will be helpful as a reference genome for future studies on the evolutionary history of the species, the genetic architecture of physiological and sex-determination traits, and the analysis of the changes in genetic diversity and composition of cultivated stocks.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140051037","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