Journal of Heredity最新文献_第2页

Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli). 转录组学的敏感性：不同样本和方法改变了海湾琵琶鱼（Syngnathus scovelli）的结论。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-15 DOI: 10.1093/jhered/esae067

Bernadette D Johnson, Emily Rose, Adam G Jones

{"title":"Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli).","authors":"Bernadette D Johnson, Emily Rose, Adam G Jones","doi":"10.1093/jhered/esae067","DOIUrl":"https://doi.org/10.1093/jhered/esae067","url":null,"abstract":"Transcriptome analysis has become a central tool in evolutionary and functional genomics. However, variation among biological samples and analysis techniques can greatly influence results, potentially compromising insights into the phenomenon under study. Here, we evaluate differences in the brain transcriptome between female and male Gulf pipefish (Syngnathus scovelli). We perform comparisons between results from entire pipelines for brain transcriptome assembly, quantification, and analysis. We also offer a unique biological comparison between two sampling instances (Redfish Bay: n = 15, Port Lavaca: n = 7). Our results demonstrate crucial shortcomings with current experimental approaches. We found high variation within our results that was driven by both technical differences between pipelines and biological differences between pipefish samples. In our analysis of highly expressed genes, we found that the choice of methods influenced the degree of contamination or noise included in the identified genes. Notably, genes identified within the same pipeline were more similar than any other comparison. Our differential expression analysis revealed that both methodology and sampling location influenced the quantity and consistency of statistically significant transcripts. In the context of these results, we offer modifications to current practices that may increase the robustness of transcriptome-based conclusions. In particular, the use of a reference-guided assembly and an increase in sample sizes are likely to improve resistance to noise or error.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A chromosome-level genome assembly of the mountain lion, Puma concolor. 山狮（Puma concolor）染色体级基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-07 DOI: 10.1093/jhered/esae063

Megan A Supple, Merly Escalona, Nicolas Alexandre, Michael R Buchalski, Seth P D Riley, Justin A Dellinger, T Winston Vickers, Ruta Sahasrabudhe, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Christopher C Wilmers, Beth Shapiro

引用次数: 0

A genome assembly for the California endemic liverwort Calasterella californica. 加州特有肝草 Calasterella californica 的基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-06 DOI: 10.1093/jhered/esae065

Ixchel S González-Ramírez, Merly Escalona, Courtney Miller, Noravit Chumchim, Mohan P A Marimuthu, Oanh Nguyen, Michael J Song, Brent D Mishler

{"title":"A genome assembly for the California endemic liverwort Calasterella californica.","authors":"Ixchel S González-Ramírez, Merly Escalona, Courtney Miller, Noravit Chumchim, Mohan P A Marimuthu, Oanh Nguyen, Michael J Song, Brent D Mishler","doi":"10.1093/jhered/esae065","DOIUrl":"https://doi.org/10.1093/jhered/esae065","url":null,"abstract":"Calasterella californica belongs to a monotypic genus of liverworts endemic to the west coast of North America, primarily distributed in California. This dioicous species occurs in a variety of ecosystems from deserts to redwood forest; little is known about how this species is adapted to live in those seemingly contrasting environments. In this paper, we report the assembly of the nuclear genome of Calasterella californica. As part of the California Conservation Genomics Project (CCGP), we used Pacific Biosciences HiFi long-read sequencing data to produce a de novo assembly that consists of 772 contigs, with a total length of 517 Mbp and a BUSCO complete score of 95%. C. californica is only the sixth species of liverworts - a group with more than 7200 described species - to have a nuclear reference genome. The availability of this reference genome will facilitate the study of the unique features of C. californica and other liverworts, pave the road towards a comparative understanding of liverwort genomes, and add an important starting point for studies of the geographic variation of this species within the CCGP project.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592313","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

Lopez, J. V. (2023). Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea, Uncovering Buried Treasures and the Value of the Benthos. Academic Press, 253 pages. Lopez, J. V. (2023).从珊瑚礁到深海的生物多样性评估与保护》，《发现埋藏的宝藏和底栖生物的价值》。学术出版社，253 页。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-05 DOI: 10.1093/jhered/esae062

A Schulze

引用次数: 0

Major Histocompatibility Complex Class II Genes Allele Diversity in Landlocked Seals. 内陆海豹的主要组织相容性复合体 II 类基因等位基因多样性。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-02 DOI: 10.1093/jhered/esae064

Ilya G Meschersky, Sergey I Meschersky, Natalia V Kryukova, Maria A Solovyeva, Evgeniy A Boltnev, Fedor V Klimov, Viatcheslav V Rozhnov

{"title":"Major Histocompatibility Complex Class II Genes Allele Diversity in Landlocked Seals.","authors":"Ilya G Meschersky, Sergey I Meschersky, Natalia V Kryukova, Maria A Solovyeva, Evgeniy A Boltnev, Fedor V Klimov, Viatcheslav V Rozhnov","doi":"10.1093/jhered/esae064","DOIUrl":"https://doi.org/10.1093/jhered/esae064","url":null,"abstract":"The allelic diversity of exon 2 (DQB gene) and exon 3 (DRB gene) of major histocompatibility complex class II was studied for the first time in two species of the landlocked pinnipeds, Baikal (N = 79) and Caspian (N = 32) seals, and these were in compared with the widespread Arctic species, the ringed seal (N = 13). The analysis of the second exon comprising the antigen-binding region revealed high allelic diversity in all three species but the pattern of the diversity was the most specific for the Baikal seal. This species differs from the other two by the smallest number of alleles in the population, yet they have the largest number of alleles per individual and by the maximum similarity of individual genotypes. Presumably, this specificity is a consequence of the spatial and temporal homogeneity of the Lake Baikal environment. Analysis of the third exon encoding the conserved β2-domain showed that the Baikal seal differs by the greatest number of amino acid sequences per individual, while the Caspian seal has the lowest number of variants. A single variant of the β2-domain, the same as in the ringed seal, predominates in the Caspian seal, whereas in the Baikal seal the two other variants predominate. At the same time, three species-specific amino acid sequences were observed among minor variants in the Caspian seal, while only one was found in the Baikal seal. This fact may suggest a longer period of independent evolution in the Caspian seal compared to the Baikal seal.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142565371","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

Absence of heterosis for hypoxia tolerance in F1 hybrids of Tigriopus californicus. Tigriopus californicus 的 F1 代杂交种在耐缺氧性方面缺乏异质性。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-28 DOI: 10.1093/jhered/esae061

Aimee Deconinck, Olivia Madalone, Chris Willett

{"title":"Absence of heterosis for hypoxia tolerance in F1 hybrids of Tigriopus californicus.","authors":"Aimee Deconinck, Olivia Madalone, Chris Willett","doi":"10.1093/jhered/esae061","DOIUrl":"https://doi.org/10.1093/jhered/esae061","url":null,"abstract":"Hybridization produces a range of outcomes from advantageous to disadvantageous, and a goal of genetic research is to understand the gene interactions that generate these outcomes. Interactions between cytoplasmic elements, such as mitochondria, and the nucleus may be particularly vulnerable to accruing disadvantageous combinations as a result of their different rates of evolution. However, mitonuclear incompatibilities often do not have an observable effect until the F2 and later generations. We used Tigriopus californicus, a model system for mitonuclear incompatibilities that is also known for exhibiting heterosis in the F1 generation, to test whether hypoxia was more stressful for mitonuclear interactions than other environmental stressors. We generated 284 parental and 436 F1 hybrids from four population crosses (720 total) and compared parental and F1 populations for hypoxia tolerance. We observed that, on average, F1 hybrids were less likely to survive a hypoxia stress test than parental populations (Parental:F1 coefficients ranged from -0.04 to 0.14 with none significantly different from 0). This suggests that hypoxia may be a particularly intense stressor for mitonuclear coordination, and that hybridization outcomes vary by trait.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523718","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 : 2024-10-23 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":"https://doi.org/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, USA. 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":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Together inbreeding and reproductive compensation favor lethal t-haplotypes. 近亲繁殖和生殖补偿共同有利于致命的 t-单倍型。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-23 DOI: 10.1093/jhered/esae030

Manisha Munasinghe, Yaniv Brandvain

{"title":"Together inbreeding and reproductive compensation favor lethal t-haplotypes.","authors":"Manisha Munasinghe, Yaniv Brandvain","doi":"10.1093/jhered/esae030","DOIUrl":"10.1093/jhered/esae030","url":null,"abstract":"Male mice who are heterozygous for distorting and non-distorting alleles at the t-haplotype transmit the driving t-haplotype around 90% of the time-a drastic departure from Mendelian expectations. This selfish act comes at a cost. The mechanism underlying transmission distortion in this system causes severe sterility in males homozygous for the drive alleles, ultimately preventing its fixation. Curiously, many driving t-haplotypes also induce embryonic lethality in both sexes when homozygous; however, this is neither universal nor a necessity for this distortion mechanism. Charlesworth provided an adaptive explanation for the evolution of lethal t-haplotypes in a population segregating for distorting and non-distorting t alleles-if mothers compensate by replacing dead embryos with new offspring (or by transferring energy to surviving offspring), a recessive lethal can be favored because it effectively allows mothers the opportunity to trade in infertile males for potentially fertile offspring. This model, however, requires near complete reproductive compensation for the invasion of the lethal t-haplotype and produces an equilibrium frequency of lethal drivers well below what is observed in nature. We show that low levels of systemic inbreeding, which we model as brother-sister mating, allow lethal t-haplotypes to invade with much lower levels of reproductive compensation. Furthermore, inbreeding allows these lethal haplotypes to largely displace the ancestral male-sterile haplotypes. Our results show that together inbreeding and reproductive compensation move expected equilibria closer to observed haplotype frequencies in natural populations and occur under lower, potentially more reasonable, parameters.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"672-681"},"PeriodicalIF":3.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141263204","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

Germline ecology: Managed herds, tolerated flocks, and pest control. 种系生态学：管理的畜群、耐受的羊群和害虫控制。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-23 DOI: 10.1093/jhered/esae004

David Haig

引用次数: 0

Autosomal suppression of sex-ratio meiotic drive influences the dynamics of X and Y chromosome coevolution. 常染色体对性比减数分裂驱动力的抑制影响了 X 和 Y 染色体共同进化的动态。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-23 DOI: 10.1093/jhered/esae048

Anjali Gupta, Robert L Unckless

{"title":"Autosomal suppression of sex-ratio meiotic drive influences the dynamics of X and Y chromosome coevolution.","authors":"Anjali Gupta, Robert L Unckless","doi":"10.1093/jhered/esae048","DOIUrl":"10.1093/jhered/esae048","url":null,"abstract":"Sex-ratio meiotic drivers are selfish genes or gene complexes that bias the transmission of sex chromosomes resulting in skewed sex ratios. Existing theoretical models have suggested the maintenance of a four-chromosome equilibrium (with driving and standard X and suppressing and susceptible Y) in a cyclic dynamic, but studies of natural populations have failed to capture this pattern. Although there are several plausible explanations for this lack of cycling, interference from autosomal suppressors has not been studied using a theoretical population genetic framework even though autosomal suppressors and Y-linked suppressors coexist in natural populations of some species. In this study, we use a simulation-based approach to investigate the influence of autosomal suppressors on the cycling of sex chromosomes. Our findings demonstrate that the presence of an autosomal suppressor can hinder the invasion of a Y-linked suppressor under some parameter space, thereby impeding the cyclic dynamics, or even the invasion of Y-linked suppression. Even when a Y-linked suppressor invades, the presence of an autosomal suppressor can prevent cycling. Our study demonstrates the potential role of autosomal suppressors in preventing sex chromosome cycling and provides insights into the conditions and consequences of maintaining both Y-linked and autosomal suppressors.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"660-671"},"PeriodicalIF":3.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114895","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