Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Henrique do Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Laforga Vanzela
Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species E. maculosa, E. geniculata, E. parodii, E. elegans, and E. montana. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.
Eleocharis R.Br.(香蒲科)物种以全中心染色体著称,这使得核型的快速分化成为可能。有资料表明,不同 Eleocharis 物种的染色体数目和基因组大小在种内和种间存在很大差异,经常伴随着重复 DNA 部分的波动。然而,由于缺乏详细的分析,人们无法更好地了解该属的全中心性和重复 DNA 演化之间的相互作用。在我们的研究中,我们通过免疫染色法检测动点蛋白KNL1和依赖于细胞周期的翻译后修饰组蛋白H2AThr121ph和H3S10ph,证实了象鼻虫染色体的全中心性。我们进一步研究了在新测序物种E. maculosa、E. geniculata、E. parodii、E. elegans和E. montana中发现的主要卫星DNA重复序列的组成和染色体分布。在发现的六个卫星DNA重复序列中,有五个呈簇状排列,而EmaSAT14则沿染色体长度呈线状不规则分布。EmaSAT14单体在整个榄香属系统发育树中的少数物种中以少量拷贝存在。尽管如此,这些单体还是积聚在荸荠科(Maculosae)的一个局限性群体--荸荠亚属(Eleocharis)中。这些数据表明,EmaSAT14沿染色体的扩增和线状分布可能是最近在该属的一个部分中发生的。
{"title":"Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (Eleocharis, Cyperaceae).","authors":"Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Henrique do Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Laforga Vanzela","doi":"10.1139/gen-2024-0089","DOIUrl":"https://doi.org/10.1139/gen-2024-0089","url":null,"abstract":"<p><p>Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species E. maculosa, E. geniculata, E. parodii, E. elegans, and E. montana. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142284426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Crematogaster Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical Crematogaster, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five Crematogaster species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2n=22 chromosomes were observed in Crematogaster erecta Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. Crematogaster aff. erecta had 2n=28, while C. limata Smith, 1858, C. tenuicula Forel, 1904 and Crematogaster sp. had 2n = 38. The telomeric motif (TTAGG)n was found in all five species, and the (TCAGG)n motif was detected in the telomeres of C. limata. This peculiar motif was also detected in the centromeric regions of C. erecta cytotype I. The microsatellite (GA)n was dispersed in the chromosomes of all species studied which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on Crematogaster.
{"title":"Chromosomal diversity in <i>Crematogaster</i> Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest.","authors":"Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Dergam, Hilton Jeferson Alves Cardoso Aguiar","doi":"10.1139/gen-2023-0130","DOIUrl":"https://doi.org/10.1139/gen-2023-0130","url":null,"abstract":"<p><p><i>Crematogaster</i> Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical <i>Crematogaster</i>, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five <i>Crematogaster</i> species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2n=22 chromosomes were observed in <i>Crematogaster erecta</i> Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. <i>Crematogaster</i> aff. erecta had 2n=28, while<i> C. limata</i> Smith, 1858, <i>C. tenuicula</i> Forel, 1904 and <i>Crematogaster </i>sp. had 2n = 38. The telomeric motif (TTAGG)<sub>n</sub> was found in all five species, and the (TCAGG)<sub>n</sub> motif was detected in the telomeres of <i>C. limata</i>. This peculiar motif was also detected in the centromeric regions of <i>C. erecta</i> cytotype I. The microsatellite (GA)<sub>n</sub> was dispersed in the chromosomes of all species studied which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on <i>Crematogaster</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Research in understanding the role of genetics and epigenetics in plant adaptations to environmental stressors such as metals is still in its infancy. The objective of the present study is to assess the effect of nickel on DNA methylation level and distribution in white birch (Betula papyrifera Marshall) using reduced representation bisulfite sequencing (RRBS). The distribution of methylated C sites of each sample revealed that the level of methylation was much higher in CG context varying between 54% and 65%, followed by CHG (24%-31.5%), and then CHH with the methylation rate between 3.3% and 5.2%. The analysis of differentially methylated regions (DMR) revealed that nickel induced both hypermethylation and hypomethylation when compared to water. Detailed analysis showed for the first time that nickel induced a higher level of hypermethylation compared to controls, while potassium triggers a higher level of hypomethylation compared to nickel. Surprisingly, the analysis of the distribution of DMRs revealed that 38%-42% were located in gene bodies, 20%-24% in exon, 19%-20% in intron, 16%-17% in promoters, and 0.03%-0.04% in transcription start site. RRBS was successful in detecting and mapping DMR in plants exposed to nickel.
{"title":"Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (<i>Betula papyrifera</i>) exposed to nickel.","authors":"Kabwe Nkongolo, Paul Michael","doi":"10.1139/gen-2024-0019","DOIUrl":"https://doi.org/10.1139/gen-2024-0019","url":null,"abstract":"<p><p>Research in understanding the role of genetics and epigenetics in plant adaptations to environmental stressors such as metals is still in its infancy. The objective of the present study is to assess the effect of nickel on DNA methylation level and distribution in white birch (<i>Betula papyrifera</i> Marshall) using reduced representation bisulfite sequencing (RRBS). The distribution of methylated C sites of each sample revealed that the level of methylation was much higher in CG context varying between 54% and 65%, followed by CHG (24%-31.5%), and then CHH with the methylation rate between 3.3% and 5.2%. The analysis of differentially methylated regions (DMR) revealed that nickel induced both hypermethylation and hypomethylation when compared to water. Detailed analysis showed for the first time that nickel induced a higher level of hypermethylation compared to controls, while potassium triggers a higher level of hypomethylation compared to nickel. Surprisingly, the analysis of the distribution of DMRs revealed that 38%-42% were located in gene bodies, 20%-24% in exon, 19%-20% in intron, 16%-17% in promoters, and 0.03%-0.04% in transcription start site. RRBS was successful in detecting and mapping DMR in plants exposed to nickel.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Krystyn J Forbes, McIntyre A Barrera, Karsten Nielsen-Roine, Evan W Hersh, Jasmine K Janes, William L Harrower, Jamieson C Gorrell
Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms (SNPs) in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change.
{"title":"Stabilizing selection and mitochondrial heteroplasmy in the Canada lynx (<i>Lynx canadensis</i>).","authors":"Krystyn J Forbes, McIntyre A Barrera, Karsten Nielsen-Roine, Evan W Hersh, Jasmine K Janes, William L Harrower, Jamieson C Gorrell","doi":"10.1139/gen-2023-0094","DOIUrl":"https://doi.org/10.1139/gen-2023-0094","url":null,"abstract":"<p><p>Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (<i>Lynx canadensis</i>) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms (SNPs) in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-05-09DOI: 10.1139/gen-2023-0075
Nairo Farias de Farias, Ricardo José Gunski, Analía Del Valle Garnero, Andrés Delgado Cañedo, Edivaldo Herculano Correa de Oliveira, Fábio Augusto Oliveira Silva, Fabiano Pimentel Torres
Avian genomes are characterized as being more compact than other amniotes, with less diversity and density of transposable elements (TEs). In addition, birds usually show bimodal karyotypes, exhibiting a great variation in diploid numbers. Some species present unusually large sex chromosomes, possibly due to the accumulation of repetitive sequences. Avian retrotransposon-like element (AviRTE) is a long interspersed nuclear element (LINE) recently discovered in the genomes of birds and nematodes, and it is still poorly characterized in terms of chromosomal mapping and phylogenetic relationships. In this study, we mapped AviRTE isolated from the Trogon surrucura genome into the T. surrucura (TSU) karyotype. Furthermore, we analyzed the phylogenetic relationships of this LINE in birds and other vertebrates. Our results showed that the distribution pattern of AviRTE is not restricted to heterochromatic regions, with accumulation on the W chromosome of TSU, yet another species with an atypical sex chromosome and TE hybridization. The phylogenetic analysis of AviRTE sequences in birds agreed with the proposed phylogeny of species in most clades, and allowed the detection of this sequence in other species, expanding the distribution of the element.
{"title":"Chromosome mapping of retrotransposon AviRTE in a neotropical bird species: <i>Trogon surrucura</i> (Trogoniformes; Trogonidae).","authors":"Nairo Farias de Farias, Ricardo José Gunski, Analía Del Valle Garnero, Andrés Delgado Cañedo, Edivaldo Herculano Correa de Oliveira, Fábio Augusto Oliveira Silva, Fabiano Pimentel Torres","doi":"10.1139/gen-2023-0075","DOIUrl":"10.1139/gen-2023-0075","url":null,"abstract":"<p><p>Avian genomes are characterized as being more compact than other amniotes, with less diversity and density of transposable elements (TEs). In addition, birds usually show bimodal karyotypes, exhibiting a great variation in diploid numbers. Some species present unusually large sex chromosomes, possibly due to the accumulation of repetitive sequences. Avian retrotransposon-like element (AviRTE) is a long interspersed nuclear element (LINE) recently discovered in the genomes of birds and nematodes, and it is still poorly characterized in terms of chromosomal mapping and phylogenetic relationships. In this study, we mapped AviRTE isolated from the <i>Trogon surrucura</i> genome into the <i>T. surrucura</i> (TSU) karyotype. Furthermore, we analyzed the phylogenetic relationships of this LINE in birds and other vertebrates. Our results showed that the distribution pattern of AviRTE is not restricted to heterochromatic regions, with accumulation on the W chromosome of TSU, yet another species with an atypical sex chromosome and TE hybridization. The phylogenetic analysis of AviRTE sequences in birds agreed with the proposed phylogeny of species in most clades, and allowed the detection of this sequence in other species, expanding the distribution of the element.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-05-09DOI: 10.1139/gen-2023-0122
Diogo Milani, Ana Elisa Gasparotto, Vilma Loreto, Dardo A Martí, Diogo C Cabral-de-Mello
Supernumerary chromosomes (B chromosomes) have been an intriguing subject of study. Our understanding of the molecular differentiation of B chromosomes from an interpopulation perspective remains limited, with most analyses involving chromosome banding and mapping of a few sequences. To gain insights into the molecular composition, origin, and evolution of B chromosomes, we conducted cytogenetic and next-generation sequencing analysis of the repeatome in the grasshopper Abracris flavolineata across various populations. Our results unveiled the presence of B chromosomes in two newly investigated populations and described new satellite DNA sequences. While we observed some degree of genetic connection among A. flavolineata populations, our comparative analysis of genomes with and without B chromosomes provided evidence of two new B chromosome variants. These variants exhibited distinct compositions of various repeat classes, including transposable elements and satellite DNAs. Based on shared repeats, their chromosomal location, and the C-positive heterochromatin content on the B chromosome, these variants likely share a common origin but have undergone distinct molecular differentiation processes, resulting in varying degrees of heterochromatinization. Our data serve as a detailed example of the dynamic and differentiated nature of B chromosome molecular content at the interpopulation level, even when they share a common origin.
超常染色体(B 染色体)一直是一个引人入胜的研究课题。从种群间的角度来看,我们对 B 染色体分子分化的了解仍然有限,大多数分析都涉及染色体条带和少数序列的图谱绘制。为了深入了解 B 染色体的分子组成、起源和进化,我们对蚱蜢 Abracris flavolineata 不同种群的重复序列组进行了细胞遗传学和新一代测序分析。我们的研究结果揭示了两个新调查种群中 B 染色体的存在,并描述了新的卫星 DNA 序列。虽然我们观察到黄铃虫种群之间存在一定程度的遗传联系,但我们对含有和不含 B 染色体的基因组进行的比较分析提供了两个新的 B 染色体变体的证据。这些变体表现出不同的重复类组成,包括转座元件和卫星 DNA。根据共享的重复序列、它们的染色体位置以及 B 染色体上 C 阳性异染色质的含量,这些变体很可能具有共同的起源,但经历了不同的分子分化过程,导致了不同程度的异染色质化。我们的数据是 B 染色体分子含量在种群间水平的动态和分化性质的一个详细例子,即使它们有共同的起源。
{"title":"Chromosomal and genomic analysis suggests single origin and high molecular differentiation of the B chromosome of <i>Abracris flavolineata</i>.","authors":"Diogo Milani, Ana Elisa Gasparotto, Vilma Loreto, Dardo A Martí, Diogo C Cabral-de-Mello","doi":"10.1139/gen-2023-0122","DOIUrl":"10.1139/gen-2023-0122","url":null,"abstract":"<p><p>Supernumerary chromosomes (B chromosomes) have been an intriguing subject of study. Our understanding of the molecular differentiation of B chromosomes from an interpopulation perspective remains limited, with most analyses involving chromosome banding and mapping of a few sequences. To gain insights into the molecular composition, origin, and evolution of B chromosomes, we conducted cytogenetic and next-generation sequencing analysis of the repeatome in the grasshopper <i>Abracris flavolineata</i> across various populations. Our results unveiled the presence of B chromosomes in two newly investigated populations and described new satellite DNA sequences. While we observed some degree of genetic connection among <i>A. flavolineata</i> populations, our comparative analysis of genomes with and without B chromosomes provided evidence of two new B chromosome variants. These variants exhibited distinct compositions of various repeat classes, including transposable elements and satellite DNAs. Based on shared repeats, their chromosomal location, and the C-positive heterochromatin content on the B chromosome, these variants likely share a common origin but have undergone distinct molecular differentiation processes, resulting in varying degrees of heterochromatinization. Our data serve as a detailed example of the dynamic and differentiated nature of B chromosome molecular content at the interpopulation level, even when they share a common origin.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-05-09DOI: 10.1139/gen-2024-0016
Danial Asgari, Tanya Purvis, Victoria Pickens, Christopher Saski, Richard P Meisel, Dana Nayduch
Animals encounter diverse microbial communities throughout their lifetime, which exert varying selection pressures. Antimicrobial peptides (AMPs), which lyse or inhibit microbial growth, are a first line of defense against some of these microbes. Here we examine how developmental variation in microbial exposure has affected the evolution of expression and amino acid sequences of Defensins (an ancient class of AMPs) in the house fly (Musca domestica). The house fly is a well-suited model for this work because it trophically associates with varying microbial communities throughout its life history and its genome contains expanded families of AMPs, including Defensins. We identified two subsets of house fly Defensins: one expressed in larvae or pupae, and the other expressed in adults. The amino acid sequences of these two Defensin subsets form distinct monophyletic clades, and they are located in separate gene clusters in the genome. The adult-expressed Defensins evolve faster than larval/pupal Defensins, consistent with different selection pressures across developmental stages. Our results therefore suggest that varied microbial communities encountered across life history can shape the evolutionary trajectories of immune genes.
{"title":"Expression of defensin genes across house fly (<i>Musca domestica</i>) life history gives insight into immune system subfunctionalization.","authors":"Danial Asgari, Tanya Purvis, Victoria Pickens, Christopher Saski, Richard P Meisel, Dana Nayduch","doi":"10.1139/gen-2024-0016","DOIUrl":"10.1139/gen-2024-0016","url":null,"abstract":"<p><p>Animals encounter diverse microbial communities throughout their lifetime, which exert varying selection pressures. Antimicrobial peptides (AMPs), which lyse or inhibit microbial growth, are a first line of defense against some of these microbes. Here we examine how developmental variation in microbial exposure has affected the evolution of expression and amino acid sequences of Defensins (an ancient class of AMPs) in the house fly (<i>Musca domestica</i>). The house fly is a well-suited model for this work because it trophically associates with varying microbial communities throughout its life history and its genome contains expanded families of AMPs, including Defensins. We identified two subsets of house fly Defensins: one expressed in larvae or pupae, and the other expressed in adults. The amino acid sequences of these two Defensin subsets form distinct monophyletic clades, and they are located in separate gene clusters in the genome. The adult-expressed Defensins evolve faster than larval/pupal Defensins, consistent with different selection pressures across developmental stages. Our results therefore suggest that varied microbial communities encountered across life history can shape the evolutionary trajectories of immune genes.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-04-29DOI: 10.1139/gen-2023-0136
Miguel Ángel Velázquez-Flores, Ruth Ruiz Esparza-Garrido
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
{"title":"Fragments derived from non-coding RNAs: how complex is genome regulation?","authors":"Miguel Ángel Velázquez-Flores, Ruth Ruiz Esparza-Garrido","doi":"10.1139/gen-2023-0136","DOIUrl":"10.1139/gen-2023-0136","url":null,"abstract":"<p><p>The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Avneet Kaur Chhina, Niloufar Abhari, Arne Mooers, Jayme Lewthwaite
We unified the recent literature with the goal to contribute to the discussion on how genetic diversity might best be conserved. We argue that this decision will be guided by how genomic variation is distributed among manageable populations (i.e. its spatial structure), the degree to which adaptive potential is best predicted by variation across the entire genome or the subset of that variation that is identified as putatively adaptive (i.e. its genomic structure), and whether we are managing species as single entities or as collections of diversifying lineages. The distribution of genetic variation and our ultimate goal will have practical implications for on-the-ground management. If adaptive variation is largely polygenic or responsive to change, its spatial structure might be broadly governed by the forces determining genome-wide variation (linked selection, drift, and gene flow), making measurement and prioritization straightforward. If we are managing species as single entities, then population-level prioritization schemes are possible so as to maximize future pooled genetic variation. We outline one such scheme based on the popular Shapley Value from cooperative game theory that considers the relative genetic contribution of a population to an unknown future collection of populations.
{"title":"Linking the spatial and genomic structure of adaptive potential for conservation management: a review.","authors":"Avneet Kaur Chhina, Niloufar Abhari, Arne Mooers, Jayme Lewthwaite","doi":"10.1139/gen-2024-0036","DOIUrl":"https://doi.org/10.1139/gen-2024-0036","url":null,"abstract":"<p><p>We unified the recent literature with the goal to contribute to the discussion on how genetic diversity might best be conserved. We argue that this decision will be guided by how genomic variation is distributed among manageable populations (i.e. its spatial structure), the degree to which adaptive potential is best predicted by variation across the entire genome or the subset of that variation that is identified as putatively adaptive (i.e. its genomic structure), and whether we are managing species as single entities or as collections of diversifying lineages. The distribution of genetic variation and our ultimate goal will have practical implications for on-the-ground management. If adaptive variation is largely polygenic or responsive to change, its spatial structure might be broadly governed by the forces determining genome-wide variation (linked selection, drift, and gene flow), making measurement and prioritization straightforward. If we are managing species as single entities, then population-level prioritization schemes are possible so as to maximize future pooled genetic variation. We outline one such scheme based on the popular Shapley Value from cooperative game theory that considers the relative genetic contribution of a population to an unknown future collection of populations.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cricula trifenestrata Helfer (commonly known as Amphutukoni muga/Cricula silkworm), a wild sericigenous insect produces golden yellow silk similar to Antheraea assamensis (muga silkworm), with significant potential as a natural fiber and biomaterial. Cricula is considered as a pest as it competes for food with muga, which produces the prized golden silk. This study focuses on decoding the mitochondrial genome of C. trifenestrata using next-generation sequencing technology and includes comparative analysis with Bombycoids and other lepidopteran insects. We found that the Cricula mitogenome spans 15,425 bp and exhibits typical gene content and arrangement consistent with other Saturniids and lepidopterans. All protein-coding genes were found to undergo purifying selection, with the highest and lowest conservation observed in the cox1 and atp8 gene respectively, indicating their potential role in future evolutionary events. We identified two types of mismatches: 23 "G-U" and 6 "U-U" pairs, similar to those found in Actias selene among the Saturniids. Additionally, our study uncovered the presence of two 33 bp repeat units and a 'TTAGA' motif in the control region, in contrast to the typical 'ATAGA' motif, suggesting functional similarity with evolving sequences. Furthermore, phylogenetic analysis supports the close relationship of Cricula with other species within the Saturniidae family.
{"title":"Comparative Genomic and Phylogenetic Analysis of the Complete Mitochondrial Genome of Cricula trifenestrata (Helfer) Among Lepidopteran Insects.","authors":"Deepika Singh, Ponnala Vimal Mosahari, Pragya Sharma, Kartik Neog, Utpal Bora","doi":"10.1139/gen-2023-0037","DOIUrl":"https://doi.org/10.1139/gen-2023-0037","url":null,"abstract":"<p><p>Cricula trifenestrata Helfer (commonly known as Amphutukoni muga/Cricula silkworm), a wild sericigenous insect produces golden yellow silk similar to Antheraea assamensis (muga silkworm), with significant potential as a natural fiber and biomaterial. Cricula is considered as a pest as it competes for food with muga, which produces the prized golden silk. This study focuses on decoding the mitochondrial genome of C. trifenestrata using next-generation sequencing technology and includes comparative analysis with Bombycoids and other lepidopteran insects. We found that the Cricula mitogenome spans 15,425 bp and exhibits typical gene content and arrangement consistent with other Saturniids and lepidopterans. All protein-coding genes were found to undergo purifying selection, with the highest and lowest conservation observed in the cox1 and atp8 gene respectively, indicating their potential role in future evolutionary events. We identified two types of mismatches: 23 \"G-U\" and 6 \"U-U\" pairs, similar to those found in Actias selene among the Saturniids. Additionally, our study uncovered the presence of two 33 bp repeat units and a 'TTAGA' motif in the control region, in contrast to the typical 'ATAGA' motif, suggesting functional similarity with evolving sequences. Furthermore, phylogenetic analysis supports the close relationship of Cricula with other species within the Saturniidae family.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}