Pub Date : 2024-09-13DOI: 10.1101/2024.09.11.610878
Christoph M Deeg, Robert G Saunders, Christopher Tam, Karia Kaukinen, Shaorong Li, Arthur L Bass, Uu-a-thluk Fisheries, Kristi M Miller
Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, and citizen scientists alike. However, the lack of sampling systems enabling high filtration volumes and rapid sample collection in the field have thus far hindered broad scale eDNA studies in the ocean specifically for small and medium scale organizations. To overcome these challenges, several modular water sampling systems that utilize hollow-membrane filtration cartridges were developed by RKS laboratories and tested by the Fisheries and Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard for eDNA filtration, the hollow-membrane filtration cartridges allowed for a six-fold increase in filtration volume and threefold increase in filtration speed. The field sampling systems, which combine pumps, a programmable controller, an air pump, an ozone generator, and up to eight filters at once, enabled efficient direct eDNA filtration from diverse aquatic environments, from creeks to the open ocean. To evaluate ease of deployment, we present the results of a three day workshop where technical staff of an Indigenous resource management organization, without any prior knowledge in eDNA sampling, were trained and performed independent eDNA sample collection. The samples were analyzed by metabarcoding and qPCR to reveal the distributions of salmon and other species co-occurring in salmon ecosystems, from large ephemeral predators, to the planktonic prey of salmon, even including their pathogens. In this example study, we further observed a substantial shift in community composition in the vicinity of aquaculture facilities where marine species associated with aquaculture feed were detected in freshwater at high relative abundance. This study demonstrates how these sampling systems provide an efficient entry point for small and medium scale organizations to utilize eDNA to fulfill their research and monitoring objectives.
{"title":"eDNA sampling systems for salmon ecosystem monitoring","authors":"Christoph M Deeg, Robert G Saunders, Christopher Tam, Karia Kaukinen, Shaorong Li, Arthur L Bass, Uu-a-thluk Fisheries, Kristi M Miller","doi":"10.1101/2024.09.11.610878","DOIUrl":"https://doi.org/10.1101/2024.09.11.610878","url":null,"abstract":"Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, and citizen scientists alike. However, the lack of sampling systems enabling high filtration volumes and rapid sample collection in the field have thus far hindered broad scale eDNA studies in the ocean specifically for small and medium scale organizations. To overcome these challenges, several modular water sampling systems that utilize hollow-membrane filtration cartridges were developed by RKS laboratories and tested by the Fisheries and Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard for eDNA filtration, the hollow-membrane filtration cartridges allowed for a six-fold increase in filtration volume and threefold increase in filtration speed. The field sampling systems, which combine pumps, a programmable controller, an air pump, an ozone generator, and up to eight filters at once, enabled efficient direct eDNA filtration from diverse aquatic environments, from creeks to the open ocean. To evaluate ease of deployment, we present the results of a three day workshop where technical staff of an Indigenous resource management organization, without any prior knowledge in eDNA sampling, were trained and performed independent eDNA sample collection. The samples were analyzed by metabarcoding and qPCR to reveal the distributions of salmon and other species co-occurring in salmon ecosystems, from large ephemeral predators, to the planktonic prey of salmon, even including their pathogens. In this example study, we further observed a substantial shift in community composition in the vicinity of aquaculture facilities where marine species associated with aquaculture feed were detected in freshwater at high relative abundance. This study demonstrates how these sampling systems provide an efficient entry point for small and medium scale organizations to utilize eDNA to fulfill their research and monitoring objectives.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.08.611878
Scott A. Ford, Rob W. Ness, Moonhyuk Kwon, Dae-Kyun Ro, Michael A. Phillips
Background: Diviners sage (Salvia divinorum; Lamiaceae) is the source of the powerful hallucinogen salvinorin A (SalA). This neoclerodane diterpenoid is an agonist of the human kappa opioid receptor with potential medical applications in the treatment of chronic pain, addiction, and post-traumatic stress disorder. Only two steps of the approximately twelve step biosynthetic sequence leading to SalA have been resolved to date. Results: To facilitate pathway elucidation in this ethnomedicinal plant species, here we report a chromosome level genome assembly. A high-quality genome sequence was assembled with an N50 value of 41.4 Mb and a BUSCO completeness score of 98.4%. The diploid (2n = 22) genome of ~541 Mb is comparable in size and ploidy to most other members of this genus. Two diterpene biosynthetic gene clusters were identified and are highly enriched in previously unidentified cytochrome P450s as well as crotonolide G synthase, which forms the dihydrofuran ring early in the SalA pathway. Coding sequences for other enzyme classes with likely involvement in downstream steps of the SalA pathway (BAHD acyl transferases, alcohol dehydrogenases, and O-methyl transferases) were scattered throughout the genome with no clear indication of clustering. Differential gene expression analysis suggests that most of these genes are not inducible by methyl jasmonate treatment. Conclusions: This genome sequence and associated gene annotation are among the highest resolution in Salvia, a genus well known for the medicinal properties of its members. Here we have identified the cohort of genes responsible for the remaining steps in the SalA pathway. This genome sequence and associated candidate genes will facilitate the elucidation of SalA biosynthesis and enable an exploration of its full clinical potential.
背景：占卜鼠尾草（Salvia divinorum; Lamiaceae）是强力致幻剂丹酚 A（Salvinorin A，SalA）的来源。这种新蛇床子二萜是人类 kappa 阿片受体的激动剂，具有治疗慢性疼痛、成瘾和创伤后应激障碍的潜在医疗用途。在产生 SalA 的大约十二步生物合成序列中，迄今只解决了两步。结果：为了促进这一民族药用植物物种的途径阐明，我们在此报告了染色体水平的基因组组装。我们组装了一个高质量的基因组序列，其 N50 值为 41.4 Mb，BUSCO 完整性得分率为 98.4%。二倍体（2n = 22）基因组约 541 Mb，在大小和倍性方面与该属的大多数其他成员相当。发现了两个二萜生物合成基因簇，其中高度富含以前未发现的细胞色素 P450s 和巴豆内酯 G 合成酶，后者在 SalA 途径的早期形成二氢呋喃环。可能参与 SalA 途径下游步骤的其他酶类（BAHD 乙酰转移酶、醇脱氢酶和 O-甲基转移酶）的编码序列分散在整个基因组中，没有明显的聚类迹象。差异基因表达分析表明，茉莉酸甲酯处理不会诱导这些基因。结论：丹参属因其成员的药用特性而闻名，该基因组序列和相关基因注释是丹参属中分辨率最高的。在这里，我们确定了负责 SalA 途径剩余步骤的基因群。该基因组序列和相关候选基因将有助于阐明 SalA 的生物合成，并探索其全部临床潜力。
{"title":"A chromosome level reference genome of Diviners sage (Salvia divinorum) provides insight into salvinorin A biosynthesis","authors":"Scott A. Ford, Rob W. Ness, Moonhyuk Kwon, Dae-Kyun Ro, Michael A. Phillips","doi":"10.1101/2024.09.08.611878","DOIUrl":"https://doi.org/10.1101/2024.09.08.611878","url":null,"abstract":"Background: Diviners sage (Salvia divinorum; Lamiaceae) is the source of the powerful hallucinogen salvinorin A (SalA). This neoclerodane diterpenoid is an agonist of the human kappa opioid receptor with potential medical applications in the treatment of chronic pain, addiction, and post-traumatic stress disorder. Only two steps of the approximately twelve step biosynthetic sequence leading to SalA have been resolved to date. Results: To facilitate pathway elucidation in this ethnomedicinal plant species, here we report a chromosome level genome assembly. A high-quality genome sequence was assembled with an N50 value of 41.4 Mb and a BUSCO completeness score of 98.4%. The diploid (2n = 22) genome of ~541 Mb is comparable in size and ploidy to most other members of this genus. Two diterpene biosynthetic gene clusters were identified and are highly enriched in previously unidentified cytochrome P450s as well as crotonolide G synthase, which forms the dihydrofuran ring early in the SalA pathway. Coding sequences for other enzyme classes with likely involvement in downstream steps of the SalA pathway (BAHD acyl transferases, alcohol dehydrogenases, and O-methyl transferases) were scattered throughout the genome with no clear indication of clustering. Differential gene expression analysis suggests that most of these genes are not inducible by methyl jasmonate treatment. Conclusions: This genome sequence and associated gene annotation are among the highest resolution in Salvia, a genus well known for the medicinal properties of its members. Here we have identified the cohort of genes responsible for the remaining steps in the SalA pathway. This genome sequence and associated candidate genes will facilitate the elucidation of SalA biosynthesis and enable an exploration of its full clinical potential.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.09.610897
Jing Yang, Rengang Zhang, Yongpeng Ma, Yuqian Ma, Weibang Sun
The tree species Firmiana major was once dominant in the savanna vegetation of the arid hot valleys of southwest China, but was considered extinct in the wild in 1998. After eight small populations were relocated by thorough investigations between 2018 and 2020, the species was subsequently recognized as a Plant Species of Extremely Small Populations (PSESP) in China in need of urgent rescue. Moreover, due to severe human disturbance, other species in the tropical woody genus Firmiana are also endangered, and the species in this genus have almost all been listed as second-class National Protected Wild Plants in China. In order to guide future research into the conservation of this group, we present here the high-quality genome assembly of F. major. This is the first genome assembly in the genus Firmiana, and is 1.4 Gb in size. The assembly consists of 1.18 Gb repetitive sequences, 37,673 annotated genes and 31,965 coding genes.
{"title":"Genome assembly of Firmina major, an endangered savanna tree species endemic to China","authors":"Jing Yang, Rengang Zhang, Yongpeng Ma, Yuqian Ma, Weibang Sun","doi":"10.1101/2024.09.09.610897","DOIUrl":"https://doi.org/10.1101/2024.09.09.610897","url":null,"abstract":"The tree species Firmiana major was once dominant in the savanna vegetation of the arid hot valleys of southwest China, but was considered extinct in the wild in 1998. After eight small populations were relocated by thorough investigations between 2018 and 2020, the species was subsequently recognized as a Plant Species of Extremely Small Populations (PSESP) in China in need of urgent rescue. Moreover, due to severe human disturbance, other species in the tropical woody genus Firmiana are also endangered, and the species in this genus have almost all been listed as second-class National Protected Wild Plants in China. In order to guide future research into the conservation of this group, we present here the high-quality genome assembly of F. major. This is the first genome assembly in the genus Firmiana, and is 1.4 Gb in size. The assembly consists of 1.18 Gb repetitive sequences, 37,673 annotated genes and 31,965 coding genes.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"85 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.09.612080
Ashton S Holub, Sarah G Choudury, Ekaterina P. Y Andrianova, Courtney E Dresden, Ricardo Urquidi Camacho, Igor Jouline, Aman Y Husbands
Functional divergence of transcription factors (TFs) has driven cellular and organismal complexity throughout evolution, but its mechanistic drivers remain poorly understood. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two functionally diverged paralogs in the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of TFs. We show that virtually all genes bound by PHB (~99%) are also bound by CNA, ruling out occupation of distinct sets of genes as a mechanism of functional divergence. Further, genes bound and regulated by both paralogs are almost always regulated in the same direction, ruling out opposite regulation of shared targets as a mechanistic driver. Functional divergence of CNA and PHB instead results from differential usage of shared binding sites, with hundreds of uniquely regulated genes emerging from a commonly bound genetic network. Regulation of a given gene by CNA or PHB is thus a function of whether a bound site is considered 'responsive' versus 'non-responsive' by each paralog. Discrimination between responsive and non-responsive sites is controlled, at least in part, by their lipid binding START domain. This suggests a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes from a shared network architecture. Taken together, our study identifies a new mechanism of HD-ZIPIII TF paralog divergence and proposes the ubiquitously distributed START evolutionary module as a driver of functional divergence.
{"title":"START domains generate paralog-specific regulons from a single network architecture","authors":"Ashton S Holub, Sarah G Choudury, Ekaterina P. Y Andrianova, Courtney E Dresden, Ricardo Urquidi Camacho, Igor Jouline, Aman Y Husbands","doi":"10.1101/2024.09.09.612080","DOIUrl":"https://doi.org/10.1101/2024.09.09.612080","url":null,"abstract":"Functional divergence of transcription factors (TFs) has driven cellular and organismal complexity throughout evolution, but its mechanistic drivers remain poorly understood. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two functionally diverged paralogs in the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of TFs. We show that virtually all genes bound by PHB (~99%) are also bound by CNA, ruling out occupation of distinct sets of genes as a mechanism of functional divergence. Further, genes bound and regulated by both paralogs are almost always regulated in the same direction, ruling out opposite regulation of shared targets as a mechanistic driver. Functional divergence of CNA and PHB instead results from differential usage of shared binding sites, with hundreds of uniquely regulated genes emerging from a commonly bound genetic network. Regulation of a given gene by CNA or PHB is thus a function of whether a bound site is considered 'responsive' versus 'non-responsive' by each paralog. Discrimination between responsive and non-responsive sites is controlled, at least in part, by their lipid binding START domain. This suggests a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes from a shared network architecture. Taken together, our study identifies a new mechanism of HD-ZIPIII TF paralog divergence and proposes the ubiquitously distributed START evolutionary module as a driver of functional divergence.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.09.611609
Luz Garcia-Longoria, Arnaud Berthomieu, Olof Hellgren, Ana Rivero
The focus of mosquito-Plasmodium interactions has predominantly been centered on mosquito immunity, revealing key mechanisms by which mosquitoes attempt to combat Plasmodium infection. However, recent evidence suggests that beyond immunity, a multitude of mosquito physiological and metabolic pathways play crucial roles in determining whether the parasite completes its development within the mosquito. We review which of these metabolic pathways are potentially modulated by Plasmodium, revealing a fragmented and occasionally contradictory state of knowledge. We then present a comprehensive transcriptomic analysis of Plasmodium-infected and uninfected mosquitoes, examining gene expression of crucial genes across different stages of the parasite's development. These genes range from key enzymes and proteins involved in gut structure and function, to genes involved in egg production and resorption, salivary gland invasion and mosquito behaviour. For this purpose, we use a non-model system consisting of the avian malaria parasite Plasmodium relictum, an invasive parasite threatening bird biodiversity across the world, and its natural vector, the mosquito Culex pipiens. Our results reveal how at each stage of its development within the mosquito, Plasmodium modulates a myriad of mosquito metabolic pathways, in ways that potentially favour its survival and the completion of its life cycle. We discuss whether this constitutes sufficient evidence of parasite-driven manipulation or whether the changes are simply the mosquito's response to the infection, which the parasite may serendipitously exploit to enhance its fitness. Our study extends the comparative transcriptomic analyses of malaria-infected mosquitoes beyond human and rodent parasites, and provides insights into the degree of conservation of metabolic pathways and into the selective pressures exerted by Plasmodium parasites on their vectors.
{"title":"Beyond immunity: a transcriptomic landscape of Plasmodium's modulation of mosquito metabolic pathways","authors":"Luz Garcia-Longoria, Arnaud Berthomieu, Olof Hellgren, Ana Rivero","doi":"10.1101/2024.09.09.611609","DOIUrl":"https://doi.org/10.1101/2024.09.09.611609","url":null,"abstract":"The focus of mosquito-Plasmodium interactions has predominantly been centered on mosquito immunity, revealing key mechanisms by which mosquitoes attempt to combat Plasmodium infection. However, recent evidence suggests that beyond immunity, a multitude of mosquito physiological and metabolic pathways play crucial roles in determining whether the parasite completes its development within the mosquito. We review which of these metabolic pathways are potentially modulated by Plasmodium, revealing a fragmented and occasionally contradictory state of knowledge. We then present a comprehensive transcriptomic analysis of Plasmodium-infected and uninfected mosquitoes, examining gene expression of crucial genes across different stages of the parasite's development. These genes range from key enzymes and proteins involved in gut structure and function, to genes involved in egg production and resorption, salivary gland invasion and mosquito behaviour. For this purpose, we use a non-model system consisting of the avian malaria parasite Plasmodium relictum, an invasive parasite threatening bird biodiversity across the world, and its natural vector, the mosquito Culex pipiens. Our results reveal how at each stage of its development within the mosquito, Plasmodium modulates a myriad of mosquito metabolic pathways, in ways that potentially favour its survival and the completion of its life cycle. We discuss whether this constitutes sufficient evidence of parasite-driven manipulation or whether the changes are simply the mosquito's response to the infection, which the parasite may serendipitously exploit to enhance its fitness. Our study extends the comparative transcriptomic analyses of malaria-infected mosquitoes beyond human and rodent parasites, and provides insights into the degree of conservation of metabolic pathways and into the selective pressures exerted by Plasmodium parasites on their vectors.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.10.612032
Qinwei Kim-Wee Zhuang, Klara Bauermeister, Jose Hector Galvez Lopez, Najla AlOgayil, Enkhjin Batdorj, Fernando Pardo-Manuel de Villena, Teruko Taketo, Guillaume Bourque, Anna K Naumova
Background. Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs) that represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored. Results. Here, we report a survey of gene, lncRNA and TE expression in four organs from mice with different combinations of gonadal and genetic sex. Data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in liver. In contrast, the X-chromosome dosage alone had modest influence on sex-biased transcription across different organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y chromosome influenced TE, but not gene or lncRNA expression in liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside close (<100 kb) to sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We also tested the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals and found no evidence to support it. Conclusions. Our data show that sex-biased expression of TEs varies among organs with highest numbers of sDETEs found in liver following the trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts.
背景。有性别偏向的基因调控是表型中性双态性的基础，已在不同细胞类型和不同发育阶段进行了研究。然而，对于占哺乳动物基因组近一半并有可能影响基因组完整性和调控的转座元件（TEs）的性别偏向表达，研究仍然不足。研究结果在此，我们报告了对具有不同性腺和遗传性别组合的小鼠四个器官中基因、lncRNA 和 TE 表达的调查。数据显示，在性腺性别对转录的影响方面，不同器官之间存在明显差异，肝脏的影响最大。相比之下，尽管不能排除 X 染色体剂量与性腺性别之间的相互作用，但单独的 X 染色体剂量对不同器官的性别偏向转录影响不大。Y染色体的存在会影响TE，但不会影响肝脏中基因或lncRNA的表达。值得注意的是，90%的性别偏向TEs（sDETEs）存在于基因簇中。此外，这些集群中有54%与性别偏倚基因或lncRNA重叠或邻近（100 kb），具有相同的性别偏倚，其表达水平也高于不与其他类型性别偏倚转录本共定位的sDETE集群。我们还测试了异染色质汇假说，该假说预测 TEs 在 XX 个体中的表达量较高，但没有发现支持该假说的证据。我们的数据显示，TEs的性别偏向表达在不同器官之间存在差异，肝脏中的sDETEs数量最多，这与基因和lncRNAs的趋势一致。与其他类型的性别偏向转录本接近会增强这种表达。
{"title":"Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation","authors":"Qinwei Kim-Wee Zhuang, Klara Bauermeister, Jose Hector Galvez Lopez, Najla AlOgayil, Enkhjin Batdorj, Fernando Pardo-Manuel de Villena, Teruko Taketo, Guillaume Bourque, Anna K Naumova","doi":"10.1101/2024.09.10.612032","DOIUrl":"https://doi.org/10.1101/2024.09.10.612032","url":null,"abstract":"Background. Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs) that represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored. Results. Here, we report a survey of gene, lncRNA and TE expression in four organs from mice with different combinations of gonadal and genetic sex. Data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in liver. In contrast, the X-chromosome dosage alone had modest influence on sex-biased transcription across different organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y chromosome influenced TE, but not gene or lncRNA expression in liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside close (<100 kb) to sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We also tested the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals and found no evidence to support it.\u0000Conclusions. Our data show that sex-biased expression of TEs varies among organs with highest numbers of sDETEs found in liver following the trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.07.611794
Li Wang, Songjoon Baek, Gauri Prasad, John Wildenthal, Konnie Guo, David Sturgill, Thucnhi Truongvo, Erin Char, Gianluca Pegoraro, Katherine McKinnon, The Pancreatic Cancer Cohort Consortium, The Pancreatic Cancer Case-Control Consortium, Jason W. Hoskins, Laufey T. Amundadottir, Efsun Arda
Genetic and epigenetic variations in regulatory enhancer elements increase susceptibility to a range of pathologies. Despite recent advances, linking enhancer elements to target genes and predicting transcriptional outcomes of enhancer dysfunction remain significant challenges. Using 3D chromatin conformation assays, we generated an extensive enhancer interaction dataset for the human pancreas, encompassing more than 20 donors and five major cell types, including both exocrine and endocrine compartments. We employed a network approach to parse chromatin interactions into enhancer-promoter tree models, facilitating a quantitative, genome-wide analysis of enhancer connectivity. With these tree models, we developed a machine learning algorithm to estimate the impact of enhancer perturbations on cell type- specific gene expression in the human pancreas. Orthogonal to our computational approach, we perturbed enhancer function in primary human pancreas cells using CRISPR interference and quantified the effects at the single-cell level through RNA FISH coupled with high-throughput imaging. Our enhancer tree models enabled the annotation of common germline risk variants associated with pancreas diseases, linking them to putative target genes in specific cell types. For pancreatic ductal adenocarcinoma, we found a stronger enrichment of disease susceptibility variants within acinar cell regulatory elements, despite ductal cells historically being assumed as the primary cell-of-origin. Our integrative approach — combining cell type-specific enhancer-promoter interaction mapping, computational models and single-cell enhancer perturbation assays — produced a robust resource for studying the genetic basis of pancreas disorders.
调控增强子元件的遗传和表观遗传变异会增加对一系列病症的易感性。尽管最近取得了进展，但将增强子元件与靶基因联系起来以及预测增强子功能障碍的转录结果仍然是重大挑战。我们利用三维染色质构象测定法为人类胰腺生成了一个广泛的增强子相互作用数据集，涵盖了20多个供体和五种主要细胞类型，包括外分泌和内分泌区。我们采用网络方法将染色质相互作用解析为增强子-启动子树模型，从而促进了对增强子连通性的全基因组定量分析。利用这些树状模型，我们开发了一种机器学习算法来估计增强子扰动对人类胰腺细胞类型特异性基因表达的影响。与我们的计算方法相对应，我们利用 CRISPR 干扰技术扰乱了原代人类胰腺细胞中的增强子功能，并通过 RNA FISH 和高通量成像技术在单细胞水平上量化了其影响。我们的增强子树模型能够注释与胰腺疾病相关的常见种系风险变异，并将它们与特定细胞类型中的假定靶基因联系起来。对于胰腺导管腺癌，尽管导管细胞历来被认为是主要的原发细胞，但我们发现疾病易感性变异在针叶细胞调控元件中的富集程度更高。我们的综合方法结合了细胞类型特异性增强子-启动子相互作用图谱、计算模型和单细胞增强子扰动试验，为研究胰腺疾病的遗传基础提供了强大的资源。
{"title":"Predictive Prioritization of Enhancers Associated with Pancreas Disease Risk","authors":"Li Wang, Songjoon Baek, Gauri Prasad, John Wildenthal, Konnie Guo, David Sturgill, Thucnhi Truongvo, Erin Char, Gianluca Pegoraro, Katherine McKinnon, The Pancreatic Cancer Cohort Consortium, The Pancreatic Cancer Case-Control Consortium, Jason W. Hoskins, Laufey T. Amundadottir, Efsun Arda","doi":"10.1101/2024.09.07.611794","DOIUrl":"https://doi.org/10.1101/2024.09.07.611794","url":null,"abstract":"Genetic and epigenetic variations in regulatory enhancer elements increase susceptibility to a range of pathologies. Despite recent advances, linking enhancer elements to target genes and predicting transcriptional outcomes of enhancer dysfunction remain significant challenges. Using 3D chromatin conformation assays, we generated an extensive enhancer interaction dataset for the human pancreas, encompassing more than 20 donors and five major cell types, including both exocrine and endocrine compartments. We employed a network approach to parse chromatin interactions into enhancer-promoter tree models, facilitating a quantitative, genome-wide analysis of enhancer connectivity. With these tree models, we developed a machine learning algorithm to estimate the impact of enhancer perturbations on cell type- specific gene expression in the human pancreas. Orthogonal to our computational approach, we perturbed enhancer function in primary human pancreas cells using CRISPR interference and quantified the effects at the single-cell level through RNA FISH coupled with high-throughput imaging. Our enhancer tree models enabled the annotation of common germline risk variants associated with pancreas diseases, linking them to putative target genes in specific cell types. For pancreatic ductal adenocarcinoma, we found a stronger enrichment of disease susceptibility variants within acinar cell regulatory elements, despite ductal cells historically being assumed as the primary cell-of-origin. Our integrative approach\t— combining cell type-specific enhancer-promoter interaction mapping, computational models and single-cell enhancer perturbation assays\t— produced a robust resource for studying the genetic basis of pancreas disorders.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.08.611677
RAJEEV CHANDEL, Dheer Singh, Suneel Kumar Onteru
Despite buffaloes being primary farm animals, their reproductive performance remains poor mainly due to inaccurate estrus detection methods that ultimately has an economic impact on dairy industry as well as farmers. Recently, numerous studies showed potential of miRNAs as estrus biomarker. However, a miRNA profile of buffalo cell free saliva, a non-invasive fluid, at estrus and diestrus stages is missing. Hence, the present study was planned to identify differential levels of salivary cell free miRNAs in estrus as compared to the diestrus phase of buffalo oestrous cycle (n=3) in order to discover a possible estrus specific miRNAs as biomarkers. miRNA-Seq data analysis showed that in total 10 miRNAs i.e bta-miR-375, bta-miR-200c, bta-miR-30d, bta-let-7f, bta-miR-200a, bta-miR-12034, bta-let-7b, bta-miR-142-5p, bta-miR-2467-3p, bta-miR-30a-5p are significantly altered (log2foldchange >3 and p<0.05) during estrus in comparison to the diestrus phase in buffaloes, suggesting their estrus biomarker potential. Overall, 8 miRNAs i.e bta-miR-375 (6.87 Fold; p-value 0.003), bta-miR-200c (5.98 Fold; p-value 0.003), bta-miR-30d (4.17 Fold; p-value 0.015), bta-let-7f (3.34 Fold; p-value 0.022), bta-miR-200a (4.92 Fold; p-value 0.024), bta-miR-12034 (3.58 Fold; p-value 0.0025), bta-let-7b (3.06 Fold; p-value 0.031), bta-miR-30a-5p (4.7 Fold; p-value 0.036) were upregulated, whereas bta-miR-142-5p (-3.4 Fold; p-value 0.032) and bta-miR-2467-3p (-5.24 Fold; p-value 0.035) were downregulated during estrus. However, further validation study using qPCR is required in a large sample size in order to determine their estrus biomarker potential. In summary, our results revealed differential salivary cell free miRNAs profile during the oestrous cycle that may lead to the development of estrus specific miRNAs based point-of-care test applicable for the reproductive management of buffaloes in the field condition in the near future.
{"title":"Comparative cell free salivary miRNA profile in Bubalus bubalis between diestrus and estrus stages","authors":"RAJEEV CHANDEL, Dheer Singh, Suneel Kumar Onteru","doi":"10.1101/2024.09.08.611677","DOIUrl":"https://doi.org/10.1101/2024.09.08.611677","url":null,"abstract":"Despite buffaloes being primary farm animals, their reproductive performance remains poor mainly due to inaccurate estrus detection methods that ultimately has an economic impact on dairy industry as well as farmers. Recently, numerous studies showed potential of miRNAs as estrus biomarker. However, a miRNA profile of buffalo cell free saliva, a non-invasive fluid, at estrus and diestrus stages is missing. Hence, the present study was planned to identify differential levels of salivary cell free miRNAs in estrus as compared to the diestrus phase of buffalo oestrous cycle (n=3) in order to discover a possible estrus specific miRNAs as biomarkers. miRNA-Seq data analysis showed that in total 10 miRNAs i.e bta-miR-375, bta-miR-200c, bta-miR-30d, bta-let-7f, bta-miR-200a, bta-miR-12034, bta-let-7b, bta-miR-142-5p, bta-miR-2467-3p, bta-miR-30a-5p are significantly altered (log2foldchange >3 and p<0.05) during estrus in comparison to the diestrus phase in buffaloes, suggesting their estrus biomarker potential. Overall, 8 miRNAs i.e bta-miR-375 (6.87 Fold; p-value 0.003), bta-miR-200c (5.98 Fold; p-value 0.003), bta-miR-30d (4.17 Fold; p-value 0.015), bta-let-7f (3.34 Fold; p-value 0.022), bta-miR-200a (4.92 Fold; p-value 0.024), bta-miR-12034 (3.58 Fold; p-value 0.0025), bta-let-7b (3.06 Fold; p-value 0.031), bta-miR-30a-5p (4.7 Fold; p-value 0.036) were upregulated, whereas bta-miR-142-5p (-3.4 Fold; p-value 0.032) and bta-miR-2467-3p (-5.24 Fold; p-value 0.035) were downregulated during estrus. However, further validation study using qPCR is required in a large sample size in order to determine their estrus biomarker potential. In summary, our results revealed differential salivary cell free miRNAs profile during the oestrous cycle that may lead to the development of estrus specific miRNAs based point-of-care test applicable for the reproductive management of buffaloes in the field condition in the near future.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.09.611967
Shikai Liu, Chenyu Shi, Chenguang Chen, Ying Tan, Yuan Tian, Daniel Macqueen, Qi Li
Most bivalve genomes exhibit extensive heterozygosity and diversity, yet the origin and function of these genomic features remain unclear. As an ancient bivalve group, oysters demonstrate high ecological adaptability with diverse genomes, which serve as a good model for studies in genome diversity and evolution. Here, we report the significant contraction but highly divergent genomic landscape of Crassostrea species and highlight the association of transposable elements (TEs) activity with this genomic feature. By constructing a haplotype-resolved genome of C. sikamea, we identified the widespread presence of high divergence sequences (HDS) between the haplotype genome. Combined with population resequencing data, we underscore the role of genome divergence driven by TEs in shaping and maintaining oyster genomic diversity. By comparing haplotype genomes across C. sikamea, Pinctada fucata, Arcuatula senhousia, and Mimachlamys varia, we find that while haplotype divergence is common, its mechanisms of occurrence and maintenance differ significantly among bivalve species. Furthermore, our results show that the widespread presence of HDS not only contributes to substantial genetic variation but also influences the regulation of gene expression in oysters. The lack of conservation in allele-specific expression among individuals in oysters suggests high plasticity in haplotype polymorphism, allowing significant variation in gene regulation to supporting high phenotype plasticity and environment adaption. Overall, these findings offer novel insights into the connection between the unique genomic features and their role in adaptive evolution.
大多数双壳类动物的基因组表现出广泛的杂合性和多样性，但这些基因组特征的起源和功能仍不清楚。作为一种古老的双壳类动物，牡蛎表现出高度的生态适应性和多样化的基因组，是研究基因组多样性和进化的良好模型。在这里，我们报告了Crassostrea物种的显著收缩但高度分化的基因组景观，并强调了转座元件（TEs）活动与这一基因组特征的关联。通过构建 C. sikamea 的单倍型分辨基因组，我们发现单倍型基因组之间广泛存在高分辨序列（HDS）。结合种群重测序数据，我们强调了TE驱动的基因组分化在形成和维持牡蛎基因组多样性中的作用。通过比较 C. sikamea、Pinctada fucata、Arcuatula senhousia 和 Mimachlamys varia 的单倍型基因组，我们发现虽然单倍型分化很常见，但其发生和维持机制在双壳类物种之间存在很大差异。此外，我们的研究结果表明，HDS 的广泛存在不仅导致了大量的遗传变异，而且还影响了牡蛎基因表达的调控。牡蛎个体间等位基因特异性表达缺乏保护，这表明单体型多态性具有很高的可塑性，从而使基因调控中的重大变异能够支持高表型可塑性和环境适应性。总之，这些发现为独特的基因组特征及其在适应性进化中的作用之间的联系提供了新的见解。
{"title":"Haplotype-resolved genomes provide insights into the origin and function of genome diversity in bivalves","authors":"Shikai Liu, Chenyu Shi, Chenguang Chen, Ying Tan, Yuan Tian, Daniel Macqueen, Qi Li","doi":"10.1101/2024.09.09.611967","DOIUrl":"https://doi.org/10.1101/2024.09.09.611967","url":null,"abstract":"Most bivalve genomes exhibit extensive heterozygosity and diversity, yet the origin and function of these genomic features remain unclear. As an ancient bivalve group, oysters demonstrate high ecological adaptability with diverse genomes, which serve as a good model for studies in genome diversity and evolution. Here, we report the significant contraction but highly divergent genomic landscape of Crassostrea species and highlight the association of transposable elements (TEs) activity with this genomic feature. By constructing a haplotype-resolved genome of C. sikamea, we identified the widespread presence of high divergence sequences (HDS) between the haplotype genome. Combined with population resequencing data, we underscore the role of genome divergence driven by TEs in shaping and maintaining oyster genomic diversity. By comparing haplotype genomes across C. sikamea, Pinctada fucata, Arcuatula senhousia, and Mimachlamys varia, we find that while haplotype divergence is common, its mechanisms of occurrence and maintenance differ significantly among bivalve species. Furthermore, our results show that the widespread presence of HDS not only contributes to substantial genetic variation but also influences the regulation of gene expression in oysters. The lack of conservation in allele-specific expression among individuals in oysters suggests high plasticity in haplotype polymorphism, allowing significant variation in gene regulation to supporting high phenotype plasticity and environment adaption. Overall, these findings offer novel insights into the connection between the unique genomic features and their role in adaptive evolution.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"47 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.05.611453
Joon-Hyun Song, Ying Zeng, Liliana M Davalos, Thomas MacCarthy, Mani Larijani, Mehdi Damaghi
Carcinogenesis is an evolutionary process, and mutations can fix the selected phenotypes in selective microenvironments. Both normal and neoplastic cells are robust to the mutational stressors in the microenvironment to the extent that secure their fitness. To test the robustness of genes under a range of mutagens, we developed a sequential mutation simulator, Sinabro, to simulate single base substitution under a given mutational process. Then, we developed a pipeline to measure the robustness of genes and cells under those mutagenesis processes. We discovered significant human genome robustness to the APOBEC mutational signature SBS2, which is associated with viral defense mechanisms and is implicated in cancer. Robustness evaluations across over 70,000 sequences against 41 signatures showed higher resilience under signatures predominantly causing C-to-T (G-to-A) mutations. Principal component analysis indicates the GC content at the codon's wobble position significantly influences robustness, with increased resilience noted under transition mutations compared to transversions. Then, we tested our results in bats at extremes of the lifespan-to-mass relationship and found the long-lived bat is more robust to APOBEC than the short-lived one. By revealing APOBEC as the prime driver of robustness in the human (and other mammalian) genome, this work bolsters the key potential role of APOBECs in carcinogenesis, as well as evolved countermeasures to this innate mutagenic process. It also provides the baseline of the human and bat genome robustness under mutational processes associated with cancer.
{"title":"Human and bats genome robustness under COSMIC mutational signatures","authors":"Joon-Hyun Song, Ying Zeng, Liliana M Davalos, Thomas MacCarthy, Mani Larijani, Mehdi Damaghi","doi":"10.1101/2024.09.05.611453","DOIUrl":"https://doi.org/10.1101/2024.09.05.611453","url":null,"abstract":"Carcinogenesis is an evolutionary process, and mutations can fix the selected phenotypes in selective microenvironments. Both normal and neoplastic cells are robust to the mutational stressors in the microenvironment to the extent that secure their fitness. To test the robustness of genes under a range of mutagens, we developed a sequential mutation simulator, Sinabro, to simulate single base substitution under a given mutational process. Then, we developed a pipeline to measure the robustness of genes and cells under those mutagenesis processes. We discovered significant human genome robustness to the APOBEC mutational signature SBS2, which is associated with viral defense mechanisms and is implicated in cancer. Robustness evaluations across over 70,000 sequences against 41 signatures showed higher resilience under signatures predominantly causing C-to-T (G-to-A) mutations. Principal component analysis indicates the GC content at the codon's wobble position significantly influences robustness, with increased resilience noted under transition mutations compared to transversions. Then, we tested our results in bats at extremes of the lifespan-to-mass relationship and found the long-lived bat is more robust to APOBEC than the short-lived one. By revealing APOBEC as the prime driver of robustness in the human (and other mammalian) genome, this work bolsters the key potential role of APOBECs in carcinogenesis, as well as evolved countermeasures to this innate mutagenic process. It also provides the baseline of the human and bat genome robustness under mutational processes associated with cancer.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"282 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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