Journal of Heredity最新文献_第3页

Comparison of dN/dS ratios shows little evidence for faster-Z effect in Furcifer chameleons after controlling for gene-specific evolutionary rates. 对 dN/dS 比率的比较表明，在控制了基因特异性进化速度之后，几乎没有证据表明变色龙中存在快 Z 效应。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-22 DOI: 10.1093/jhered/esae070

Lucija Andjel, Lukáš Kratochvíl, Michail Rovatsos

{"title":"Comparison of dN/dS ratios shows little evidence for faster-Z effect in Furcifer chameleons after controlling for gene-specific evolutionary rates.","authors":"Lucija Andjel, Lukáš Kratochvíl, Michail Rovatsos","doi":"10.1093/jhered/esae070","DOIUrl":"https://doi.org/10.1093/jhered/esae070","url":null,"abstract":"The faster-X/Z effect hypothesis states that genes linked to X/Z chromosomes should accumulate mutations faster than autosomal genes. Although faster evolution of X/Z-linked genes has been reported in several plant and animal lineages, conflicting results have been reported in others. We examined the faster-Z effect in chameleons of the genus Furcifer, a lineage with differentiated ZZ/ZW chromosomes for at least 20 million years. We sequenced the genomes of four species of Furcifer chameleons in the Illumina platform and compared the substitution rates of synonymous and non-synonymous mutations and their ratios among autosomal, Z-specific, and pseudoautosomal protein-coding genes. The inclusion of two chameleon outgroups lacking the differentiated ZZ/ZW sex chromosomes allowed us to control for gene-specific evolutionary rates that might confound the testing of the faster-X/Z effect. Significant differences in evolutionary rates were found between autosomal, Z-specific, and pseudoautosomal genes of Furcifer chameleons. However, the inclusion of the outgroups with different sex chromosomes suggests that these genes had different evolutionary rates prior to their incorporation into the differentiated ZZ/ZW sex chromosomes of the Furcifer genus. The results highlight the need to control for differences in the evolutionary rates of individual genes when testing for the faster X/Z effect.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689693","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

Plumage polymorphism in the black sparrowhawk (Accipiter melanoleucus) is strongly associated with expression level of agouti signalling protein. 黑雀鹰（Accipiter melanoleucus）的羽毛多态性与agouti信号蛋白的表达水平密切相关。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-18 DOI: 10.1093/jhered/esae068

Edmund Rodseth, Arjun Amar, Petra Sumasgutner, Robert A Ingle

{"title":"Plumage polymorphism in the black sparrowhawk (Accipiter melanoleucus) is strongly associated with expression level of agouti signalling protein.","authors":"Edmund Rodseth, Arjun Amar, Petra Sumasgutner, Robert A Ingle","doi":"10.1093/jhered/esae068","DOIUrl":"https://doi.org/10.1093/jhered/esae068","url":null,"abstract":"Melanin-based plumage polymorphisms in birds are often associated with mutations in the melanogenesis genes, notably the melanocortin-1 receptor (MC1R), but may also arise through changes in the expression of these genes. Here we investigate the molecular basis of plumage polymorphism in both adult and juvenile black sparrowhawks (Accipiter melanoleucus), an African raptor that occurs in two adult colour morphs, light and dark, and also exhibits variation in juvenile plumage colouration. Our results confirmed that plumage differences in adult morphs were a result of differential deposition of eumelanin in their ventral contour feathers. No polymorphisms in the coding regions of the MC1R or the agouti signalling protein (ASIP) genes associated with adult colour morph were identified. However, lack of pigmentation in the developing breast feathers of light morph birds was strongly associated with elevated ASIP expression, and concomitant down-regulation of the downstream melanogenesis genes microphthalmia-associated transcription factor (MITF), tyrosinase (TYR) and tyrosinase-related protein 1 (TYRP1). Variation in the rufous coloured plumage of juveniles was found to be due to covariation in eumelanin and pheomelanin levels in dorsal and ventral contour feathers. As in adult birds, an inverse relationship between melanin pigmentation and ASIP expression was observed. This covariation between eumelanin and pheomelanin levels is not consistent with the pigment type-switching model of melanogenesis, where increased ASIP expression results in a switch from eumelanin to pheomelanin production. This highlights the need for caution when extrapolating results from model systems to other animals and the value of conducting research in wild species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649486","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

Transposable element accumulation drives genome size increase in Hylesia metabus (Lepidoptera: Saturniidae), an urticating moth species from South America. 可转座元件的积累推动了南美洲荨麻蛾物种 Hylesia metabus（鳞翅目：土星科）基因组大小的增加。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-18 DOI: 10.1093/jhered/esae069

Charles Perrier, Rémi Allio, Fabrice Legeai, Mathieu Gautier, Frédéric Bénéluz, William Marande, Anthony Theron, Nathalie Rodde, Melfran Herrera, Laure Saune, Hugues Parrinello, Melanie Mcclure, Mónica Arias

{"title":"Transposable element accumulation drives genome size increase in Hylesia metabus (Lepidoptera: Saturniidae), an urticating moth species from South America.","authors":"Charles Perrier, Rémi Allio, Fabrice Legeai, Mathieu Gautier, Frédéric Bénéluz, William Marande, Anthony Theron, Nathalie Rodde, Melfran Herrera, Laure Saune, Hugues Parrinello, Melanie Mcclure, Mónica Arias","doi":"10.1093/jhered/esae069","DOIUrl":"https://doi.org/10.1093/jhered/esae069","url":null,"abstract":"We present the first nuclear genome assembly and a complete mitogenome for Hylesia metabus (Arthropoda; Insecta; Lepidoptera; Saturniidae). The assembled nuclear genome sequence is 1,271 Mb long, which is among the 10 largest lepidopteran genome assemblies published to date. It is scaffolded in 31 pseudo chromosomes, has a BUSCO score of 99.5%, and has a highly conserved synteny compared to phylogenetically close species. Repetitive elements make up 67% of the nuclear genome and are mainly located in intergenic regions, among which LINEs were predominant, with CR1-Zenon being the most abundant. Phylogenetic and comparative analyses of H. metabus assembly and 17 additional Saturniidae and Sphingidae assemblies suggested that an accumulation of repetitive elements likely led to the increased size of H. metabus' genome. Gene annotation using Helixer identified 26,122 transcripts. The Z scaffold was identified using both a synteny analysis and variations of coverage for two resequenced male and female H. metabus. The H. metabus nuclear genome and mitogenome assemblies can be found and browsed on the BIPAA website and constitute useful resources for future population and comparative genomics studies.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649503","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

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