Single nucleotide polymorphisms (SNPs) widely existing in different breeds genome represent population-specific. Under the influence of long-term evolution and artificial selection, there are a large number of SNPs between western lean-type pig breeds and Chinese indigenous pig breeds, but until now, little is known about their roles in inter-breed differences. Our study revealed SNP rs3471653254 C>T generated from the two types of pigs mentioned above, located in the promoter shared by MyoG and Myoparr, played an important role in the differentiation of myoblast by influencing the enrichment of HOXA5 to regulate the transcription of MyoG and Myoparr. Meanwhile, Myoparr could be used as the sponge of mir-30b-3p which repressed myogenic differentiation and muscle regeneration through targeting MyoD. Our results indicated that SNP rs3471653254 C>T is essential for myogenic differentiation and regeneration and could be used as an ideal site for increasing lean meat production in pigs.
{"title":"A causative SNP in the promoter of myogenin is essential for myogenic differentiation","authors":"Zhuhu Lin, Xiaoyu Wang, Ziyun Liang, Rong Xu, Meilin Chen, Xian Tong, Chenggan Li, Yanyun Xiong, Renqiang Yuan, Yaosheng Chen, Xiaohong Liu, Yunxiang Zhao, Delin Mo","doi":"10.1101/2024.08.01.606143","DOIUrl":"https://doi.org/10.1101/2024.08.01.606143","url":null,"abstract":"Single nucleotide polymorphisms (SNPs) widely existing in different breeds genome represent population-specific. Under the influence of long-term evolution and artificial selection, there are a large number of SNPs between western lean-type pig breeds and Chinese indigenous pig breeds, but until now, little is known about their roles in inter-breed differences. Our study revealed SNP rs3471653254 C>T generated from the two types of pigs mentioned above, located in the promoter shared by MyoG and Myoparr, played an important role in the differentiation of myoblast by influencing the enrichment of HOXA5 to regulate the transcription of MyoG and Myoparr. Meanwhile, Myoparr could be used as the sponge of mir-30b-3p which repressed myogenic differentiation and muscle regeneration through targeting MyoD. Our results indicated that SNP rs3471653254 C>T is essential for myogenic differentiation and regeneration and could be used as an ideal site for increasing lean meat production in pigs.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"194 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934553","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 : 2024-08-02DOI: 10.1101/2024.08.01.606211
Yitao Dai, Lucia Pita, Alessandra S Eustaquio
The filter feeding capacity of marine sponges contributes to biogeochemical cycling and they are also involved in habitat formation, properties that are critical to marine ecology. Sponge-associated microbes are crucial to the functional roles provided by sponges. α-Proteobacteria belonging to the Pseudovibrio genus have been isolated from many different marine sponge genera and have been proposed to contribute to sponge health. We recently reported specialized metabolites we named pseudovibriamides from Pseudovibrio brasiliensis Ab134. The pseudovibriamide encoding ppp gene cluster is found in two thirds of Pseudovibrio genomes. Pseudovibriamides coordinate motility and biofilm formation, behaviors that are known to be important for host colonization. Although reverse genetics methods to delete genes via homologous recombination have been established, no self-replicative vectors have been reported for Pseudovibrio. We show that plasmid vectors containing three different broad-host-range replicons, RSF1010, RK2, and pBBR1, can be used in P. brasiliensis for fluorescent protein expression and consequent labeling. We then applied GFP and mCherry expressing strains to answer the question of whether pseudovibriamides affect the uptake of P. brasiliensis by Aplysina aerophoba sponges. P. brasiliensis cell counts decreased in the sponge aquaria at an equivalent rate for wild-type and pseudovibriamide-defective ΔpppA mutant strains, indicating that the sponge filters each strain indiscriminately under the conditions tested. Yet, the filtering capacity varied for each sponge individual tested, stressing the importance of performing experiments with wild-type and mutant bacterial strains in the same aquarium to allow for rigorous conclusions, which is now enabled with the methods established here.
{"title":"Evaluation of vectors for gene expression in Pseudovibrio bacteria and their application in Aplysina marine sponge studies","authors":"Yitao Dai, Lucia Pita, Alessandra S Eustaquio","doi":"10.1101/2024.08.01.606211","DOIUrl":"https://doi.org/10.1101/2024.08.01.606211","url":null,"abstract":"The filter feeding capacity of marine sponges contributes to biogeochemical cycling and they are also involved in habitat formation, properties that are critical to marine ecology. Sponge-associated microbes are crucial to the functional roles provided by sponges. α-Proteobacteria belonging to the <em>Pseudovibrio</em> genus have been isolated from many different marine sponge genera and have been proposed to contribute to sponge health. We recently reported specialized metabolites we named pseudovibriamides from <em>Pseudovibrio brasiliensis</em> Ab134. The pseudovibriamide encoding <em>ppp</em> gene cluster is found in two thirds of <em>Pseudovibrio</em> genomes. Pseudovibriamides coordinate motility and biofilm formation, behaviors that are known to be important for host colonization. Although reverse genetics methods to delete genes via homologous recombination have been established, no self-replicative vectors have been reported for <em>Pseudovibrio</em>. We show that plasmid vectors containing three different broad-host-range replicons, RSF1010, RK2, and pBBR1, can be used in <em>P. brasiliensi</em>s for fluorescent protein expression and consequent labeling. We then applied GFP and mCherry expressing strains to answer the question of whether pseudovibriamides affect the uptake of <em>P. brasiliensis</em> by <em>Aplysina aerophoba</em> sponges. <em>P. brasiliensis</em> cell counts decreased in the sponge aquaria at an equivalent rate for wild-type and pseudovibriamide-defective Δ<em>pppA</em> mutant strains, indicating that the sponge filters each strain indiscriminately under the conditions tested. Yet, the filtering capacity varied for each sponge individual tested, stressing the importance of performing experiments with wild-type and mutant bacterial strains in the same aquarium to allow for rigorous conclusions, which is now enabled with the methods established here.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141881588","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 : 2024-07-31DOI: 10.1101/2024.07.30.605898
Parvathy Surendranadh, Himani Sachdeva
Assortative mating and sexual selection are widespread in nature and can play an important role in speciation, through the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified. Here, we consider a polygenic `magic' trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at individual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early generation hybrids. Our analysis clarifies how `tipping points' (characterised by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene flow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI.
同类交配和性选择在自然界非常普遍，通过建立和维持生殖隔离（RI），它们在物种形成过程中发挥着重要作用。然而，它们在 RI 期间对全基因组基因流抑制的贡献却很少被量化。在此，我们考虑了一种多基因 "神奇 "性状，这种性状在通过迁移连接的两个种群中进行分化选择，同时也是同配交配的基础，从而对一个或两个性别产生性选择。我们假定所有其他基因位点对任何基因位点的影响都可以通过有效迁移率来囊括，从而对单个性状位点的分化进行理论预测。我们的分析阐明了 "临界点"（以适应性分化的突然崩溃为特征）是如何出现的，以及同类交配何时可以改变迁移的临界水平，从而使分化崩溃。我们量化了生存能力和性选择对全基因组基因流动障碍的相对贡献，并讨论了这些贡献如何取决于现有的分化水平。我们的研究结果表明，有效迁移率是理解基因组分化的一种有用方法，即使在涉及多种相互作用的 RI 机制的情况下也是如此。
{"title":"Effect of assortative mating and sexual selection on polygenic barriers to gene flow","authors":"Parvathy Surendranadh, Himani Sachdeva","doi":"10.1101/2024.07.30.605898","DOIUrl":"https://doi.org/10.1101/2024.07.30.605898","url":null,"abstract":"Assortative mating and sexual selection are widespread in nature and can play an important role in speciation, through the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified. Here, we consider a polygenic `magic' trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at individual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early generation hybrids. Our analysis clarifies how `tipping points' (characterised by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene flow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862852","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 : 2024-07-31DOI: 10.1101/2024.07.30.605883
Yan Zhao, Andrea Fernández-Montoro, Greet Peeters, Tatjana Jatsenko, Tine De Coster, Daniel Angel-Velez, Thomas Lefevre, Thierry Voet, Olga Tšuiko, Ants Kurg, Katrien Smits, Ann Van Soom, Joris Robert Vermeesch
Whole-genome (WG) abnormalities, such as uniparental diploidy and triploidy, cause fetal death. Occasionally, they coexist with biparental diploid cells in live births. Understanding the origin and early development of WG abnormal blastomeres is crucial for explaining the formation of androgenotes, gynogenotes, triploidy, chimerism, and mixoploidy. By haplotyping 118 blastomeres from first cleavages, we identified various mechanisms of heterogoneic divisions that lead to WG abnormal blastomeres or their coexistence with normal blastomeres in both multipolar and bipolar cleaving zygotes. After culturing the totipotent blastomeres to three preimplantation stages and performing transcriptome profiling on over 600 cells, we discovered that stress responses contribute to developmental impairment in WG abnormal cells, resulting in either cell arrest or blastocyst formation. However, first-cleavage-derived WG abnormal blastomeres can survive early development and progress to blastocysts. Their potential dominance in preimplantation embryos represents an overlooked cause of abnormal development. Haplotype based screening could further increase pregnancy rates.
全基因组（WG）异常，如单亲二倍体和三倍体，会导致胎儿死亡。在活产中，它们偶尔会与双亲二倍体细胞共存。了解 WG 异常胚泡的起源和早期发育，对于解释雄激素、雌激素、三倍体、嵌合体和混合倍性的形成至关重要。通过对来自第一裂殖的 118 个胚泡进行单倍型分析，我们确定了导致 WG 异常胚泡或在多极性和双极性裂殖合子中与正常胚泡共存的各种异源分裂机制。在将全能胚泡培养到三个植入前阶段并对 600 多个细胞进行转录组分析后，我们发现应激反应导致 WG 异常细胞发育受损，导致细胞停滞或胚泡形成。然而，第一次裂解衍生的 WG 异常胚泡能在早期发育中存活下来并发育成胚泡。它们在植入前胚胎中的潜在优势是被忽视的异常发育原因。基于单倍型的筛查可进一步提高妊娠率。
{"title":"Mechanistic origin and preimplantation development of uniparental and polyploid blastomeres","authors":"Yan Zhao, Andrea Fernández-Montoro, Greet Peeters, Tatjana Jatsenko, Tine De Coster, Daniel Angel-Velez, Thomas Lefevre, Thierry Voet, Olga Tšuiko, Ants Kurg, Katrien Smits, Ann Van Soom, Joris Robert Vermeesch","doi":"10.1101/2024.07.30.605883","DOIUrl":"https://doi.org/10.1101/2024.07.30.605883","url":null,"abstract":"Whole-genome (WG) abnormalities, such as uniparental diploidy and triploidy, cause fetal death. Occasionally, they coexist with biparental diploid cells in live births. Understanding the origin and early development of WG abnormal blastomeres is crucial for explaining the formation of androgenotes, gynogenotes, triploidy, chimerism, and mixoploidy. By haplotyping 118 blastomeres from first cleavages, we identified various mechanisms of heterogoneic divisions that lead to WG abnormal blastomeres or their coexistence with normal blastomeres in both multipolar and bipolar cleaving zygotes. After culturing the totipotent blastomeres to three preimplantation stages and performing transcriptome profiling on over 600 cells, we discovered that stress responses contribute to developmental impairment in WG abnormal cells, resulting in either cell arrest or blastocyst formation. However, first-cleavage-derived WG abnormal blastomeres can survive early development and progress to blastocysts. Their potential dominance in preimplantation embryos represents an overlooked cause of abnormal development. Haplotype based screening could further increase pregnancy rates.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"187 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862853","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}
Rape (Brassica napus L.) is a major oil crop in our country, valued for its oil and ornamental uses. This study analyzed 35 ornamental rape germplasm resources from different origins to examine differences in agronomic traits and molecular markers. Nine agronomic traits were assessed in the field for variability, correlation, principal component analysis, and cluster analysis. Genetic diversity was analyzed using microsatellite (ISSR) markers and the unweighted pair group method with arithmetic mean (UPGMA). Our findings revealed a notable average coefficient of variation of 22.59% across the nine agronomic traits, with flower color exhibiting the highest variability and corolla width the least. The observed range of variation spanned from 9.24% to 83.38%, the correlation among these traits was generally low, with a mere 13.9% demonstrating significant correlations. The four principal components accounted for an impressive 84.62% of the cumulative contribution rate, while the genetic similarity, as gauged by eight ISSR primers, varied from 0.675 to 0.980. Most strikingly, we observed that plants from the same geographical region displayed molecular-level differences, underscoring the rich genetic diversity inherent in the 35 ornamental rape resources under study. Employing UPGMA cluster analysis on the primary agronomic traits and ISSR molecular markers, the 35 ornamental rape resources were categorized into seven and four distinct groups, respectively. Although the clustering outcomes from these two methodologies did not align perfectly, they served to complement each other. Collectively, these insights offer a theoretical framework for the innovation of ornamental rape germplasm resources and the cultivation of novel varieties.
{"title":"Genetic diversity analysis of main agronomic traits and ISSR markers in 35 ornamental rape germplasm resources","authors":"Mang Xia, Meizhu Chen, Xiaoxiao Dong, Miao Chen, Jingdong Chen, Heping Wang, Yuanhuo Dong, Changli Zeng, Xigang Dai, Meizhu Chen,Xiaoxiao Dong, Jingdong Chen, Miao Cheng, Heping Wan, Yuanhuo Dong, Changli Zeng and Xig","doi":"10.1101/2024.07.29.605676","DOIUrl":"https://doi.org/10.1101/2024.07.29.605676","url":null,"abstract":"Rape (Brassica napus L.) is a major oil crop in our country, valued for its oil and ornamental uses. This study analyzed 35 ornamental rape germplasm resources from different origins to examine differences in agronomic traits and molecular markers. Nine agronomic traits were assessed in the field for variability, correlation, principal component analysis, and cluster analysis. Genetic diversity was analyzed using microsatellite (ISSR) markers and the unweighted pair group method with arithmetic mean (UPGMA). Our findings revealed a notable average coefficient of variation of 22.59% across the nine agronomic traits, with flower color exhibiting the highest variability and corolla width the least. The observed range of variation spanned from 9.24% to 83.38%, the correlation among these traits was generally low, with a mere 13.9% demonstrating significant correlations. The four principal components accounted for an impressive 84.62% of the cumulative contribution rate, while the genetic similarity, as gauged by eight ISSR primers, varied from 0.675 to 0.980. Most strikingly, we observed that plants from the same geographical region displayed molecular-level differences, underscoring the rich genetic diversity inherent in the 35 ornamental rape resources under study. Employing UPGMA cluster analysis on the primary agronomic traits and ISSR molecular markers, the 35 ornamental rape resources were categorized into seven and four distinct groups, respectively. Although the clustering outcomes from these two methodologies did not align perfectly, they served to complement each other. Collectively, these insights offer a theoretical framework for the innovation of ornamental rape germplasm resources and the cultivation of novel varieties.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"64 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862760","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}
Connecting genetic variation to phenotypes and understanding the underlying biological mechanisms has been a fundamental goal of biological genetics. Here, we used the association analysis to identify a Vip3Aa resistance-associated genomic region in a strain of fall armyworm, JC-R, which exhibits >5000-fold resistance to the Bt toxin Vip3Aa. However, through various analytical approaches and fine-scale mapping across different populations, we demonstrated that this genomic region exhibits strong genetic linkage. The chromosome-level genome of JC-R and its parent strain JC-S were assembled, and extensive structural variations in the linkage regions were identified, which could be responsible for maintaining the linkage. To identify the causal variation within this linked region, a chromosome fragment stepwise knockout strategy based on CRISPR/Cas9 was developed. By crossing with the resistant strain and phenotyping segregating offspring on Vip3Aa-containing diet, we identified a chromosomal segment, KO8, containing the resistant gene. Subsequently, we conducted a comprehensive analysis of the variations in the KO8 region using multi-omics approaches, including genomic data, RNA-seq, proteomic, PacBio long read Iso-seq, and phosphoproteomic data. This analysis identified multiple variations in the chitin synthase gene CHS2, including amino acid substitution, alternative splicing, and changes in phosphorylation sites. After knocking out the CHS2, larvae exhibited over 6777-fold resistance to Vip3Aa. These results demonstrate that the chromosome fragment stepwise knockout strategy is a viable approach for studying complex genomic regions, and highlight the value of comprehensive analysis of genetic variations using multi-omics data. The identified candidate gene could potentially advance monitoring and management of pest resistance to Vip3Aa.
{"title":"CRISPR-mediated chromosome deletion facilitates genetic mapping of Vip3Aa resistance gene within complex genomic region in an invasive global pest","authors":"Minghui Jin, Yinxue Shan, Yan Peng, Shenlin Chen, Xuanhe Zhou, Kaiyu Liu, Yutao Xiao","doi":"10.1101/2024.07.30.605831","DOIUrl":"https://doi.org/10.1101/2024.07.30.605831","url":null,"abstract":"Connecting genetic variation to phenotypes and understanding the underlying biological mechanisms has been a fundamental goal of biological genetics. Here, we used the association analysis to identify a Vip3Aa resistance-associated genomic region in a strain of fall armyworm, JC-R, which exhibits >5000-fold resistance to the Bt toxin Vip3Aa. However, through various analytical approaches and fine-scale mapping across different populations, we demonstrated that this genomic region exhibits strong genetic linkage. The chromosome-level genome of JC-R and its parent strain JC-S were assembled, and extensive structural variations in the linkage regions were identified, which could be responsible for maintaining the linkage. To identify the causal variation within this linked region, a chromosome fragment stepwise knockout strategy based on CRISPR/Cas9 was developed. By crossing with the resistant strain and phenotyping segregating offspring on Vip3Aa-containing diet, we identified a chromosomal segment, KO8, containing the resistant gene. Subsequently, we conducted a comprehensive analysis of the variations in the KO8 region using multi-omics approaches, including genomic data, RNA-seq, proteomic, PacBio long read Iso-seq, and phosphoproteomic data. This analysis identified multiple variations in the chitin synthase gene CHS2, including amino acid substitution, alternative splicing, and changes in phosphorylation sites. After knocking out the CHS2, larvae exhibited over 6777-fold resistance to Vip3Aa. These results demonstrate that the chromosome fragment stepwise knockout strategy is a viable approach for studying complex genomic regions, and highlight the value of comprehensive analysis of genetic variations using multi-omics data. The identified candidate gene could potentially advance monitoring and management of pest resistance to Vip3Aa.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862854","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}
Understanding the mechanisms driving centromere evolution is crucial for deciphering eukaryotic evolution and speciation processes. Despite their widely recognized characteristics of conserved function in cell division, the centromeres have showed high diversity in composition and structure between species. The mechanism underlying this paradox remain poorly understood. Here, we assembled 67 high-quality rice genomes from Oryza AA group, encompassing both Asian and African rice species, and conducted an extensive analysis of over 800 nearly complete centromeres. Through de novo annotation of satellite sequences and employing a progressive compression strategy, we quantified the local homogenization and multi-layer nested structures of rice centromeres and found that genetic innovations in rice centromeres primarily arise from internal structural variations and retrotransposon insertions, along with a certain number of non-canonical satellite repeats (sati). Despite these rapid structural alterations, the single-base substitution rate in rice centromeres appears relatively lower compared to the chromosome arms. Contrary to the KARMA model for Arabidopsis centromere evolution, our model (RICE) suggests that centrophilic LTRs contribute to the decline of progenitor centromeres composed of satellite repeats, and facilitate the formation of evolutionary neo-centromeres, which are enriched with extended CENH3 binding regions beyond the native satellite arrays in plant genomes. In summary, this study provides novel insights into genomic divergence and reproductive barriers among rice species and subspecies, and advances our understanding of plant centromere evolution.
{"title":"Genetic diversity and evolution of rice centromeres","authors":"Lingjuan Xie, Yujie Huang, Wei Huang, lianguang Shang, Yanqing Sun, Quanyu Chen, Shuangtian Bi, Mingyu Suo, Shiyu Zhang, Chentao Yang, Xiaoming Zheng, Weiwei Jin, Qian Qian, Longjiang Fan, Wu Dongya","doi":"10.1101/2024.07.28.605524","DOIUrl":"https://doi.org/10.1101/2024.07.28.605524","url":null,"abstract":"Understanding the mechanisms driving centromere evolution is crucial for deciphering eukaryotic evolution and speciation processes. Despite their widely recognized characteristics of conserved function in cell division, the centromeres have showed high diversity in composition and structure between species. The mechanism underlying this paradox remain poorly understood. Here, we assembled 67 high-quality rice genomes from Oryza AA group, encompassing both Asian and African rice species, and conducted an extensive analysis of over 800 nearly complete centromeres. Through de novo annotation of satellite sequences and employing a progressive compression strategy, we quantified the local homogenization and multi-layer nested structures of rice centromeres and found that genetic innovations in rice centromeres primarily arise from internal structural variations and retrotransposon insertions, along with a certain number of non-canonical satellite repeats (sati). Despite these rapid structural alterations, the single-base substitution rate in rice centromeres appears relatively lower compared to the chromosome arms. Contrary to the KARMA model for Arabidopsis centromere evolution, our model (RICE) suggests that centrophilic LTRs contribute to the decline of progenitor centromeres composed of satellite repeats, and facilitate the formation of evolutionary neo-centromeres, which are enriched with extended CENH3 binding regions beyond the native satellite arrays in plant genomes. In summary, this study provides novel insights into genomic divergence and reproductive barriers among rice species and subspecies, and advances our understanding of plant centromere evolution.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"53 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862761","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 : 2024-07-28DOI: 10.1101/2024.07.28.605483
Douglas Amado, Eva L. Koch, Erick M. G. Cordeiro, Wellingson A. Araújo, Antonio Augusto F Garcia, David G. Heckel, Gabriela Montejo-Kovacevich, Henry L. North, Alberto S. Corrêa, Chris D. Jiggins, Celso Omoto
Insecticide resistance is a major problem in food production, environmental sustainability, and human health. The cotton bollworm Helicoverpa armigera is a globally distributed crop pest affecting over 300 crop species. H. armigera has rapidly evolved insecticide resistance, making it one of the most damaging pests worldwide. Understanding the genetic basis of insecticide resistance provides insights to develop tools, such as molecular markers, that can be used to slow or prevent the evolution of resistance. We explore the genetic architecture of H. armigera resistance to a widely used insecticide, flubendiamide, using two complementary approaches: genome-wide association studies (GWAS) in wild-caught samples and quantitative trait locus (QTL) mapping in a controlled cross of susceptible and resistant laboratory strains. Both approaches identified one locus on chromosome 2, revealing two SNPs within 976 bp that can be used to monitor field resistance to flubendiamide. This was the only region identified using linkage mapping, though GWAS revealed additional sites associated with resistance. Other loci identified by GWAS in field populations contained known insecticide detoxification genes from the ATP-binding cassette family, ABCA1, ABCA3, ABCF2 and MDR1. Our findings revealed an oligogenic genetic architecture, in contrast to previous reports of monogenic resistance associated with the ryanodine receptor. This work elucidates the genetic basis of rapidly evolving insecticide resistance and will contribute to the development of effective insecticide resistance management strategies.
杀虫剂抗药性是粮食生产、环境可持续性和人类健康的一个主要问题。棉铃虫（Helicoverpa armigera）是一种分布于全球的作物害虫，影响 300 多种作物。棉铃虫迅速进化出抗药性，使其成为全球危害最大的害虫之一。了解杀虫剂抗药性的遗传基础有助于开发分子标记等工具，用于减缓或防止抗药性的进化。我们采用两种互补的方法探索了蓟马对一种广泛使用的杀虫剂氟苯虫酰胺产生抗性的遗传结构：野生捕获样本的全基因组关联研究（GWAS）和易感性与抗性实验室菌株对照杂交的定量性状位点（QTL）图谱。这两种方法都确定了 2 号染色体上的一个位点，揭示了 976 bp 范围内的两个 SNP，可用于监测野外对氟苯菌酰胺的抗性。这是利用连接图谱确定的唯一区域，尽管全球基因组分析发现了与抗性相关的其他位点。在田间种群中通过 GWAS 发现的其他位点包含 ATP 结合盒家族的已知杀虫剂解毒基因 ABCA1、ABCA3、ABCF2 和 MDR1。我们的研究结果揭示了一种寡基因遗传结构，这与以前关于与雷诺丁受体有关的单基因抗性的报道形成了鲜明对比。这项工作阐明了快速演变的杀虫剂抗药性的遗传基础，将有助于制定有效的杀虫剂抗药性管理策略。
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Pub Date : 2024-07-28DOI: 10.1101/2024.07.26.605020
Gael Moquin-Beaudry, Lovatiana Andriamboavonjy, Sebastien Audet, Laura Hamilton, Antoine Duquette, Sylvain Chouinard, Michel Panisset, Martine Tetreault
Parkinson's Disease (PD) is widely recognized for its impact on the central nervous system. Recent breakthroughs underscore the crucial role of interactions between central and peripheral systems in PD's pathogenesis, highlighting the need for a paradigm shift in PD research. The spotlight is now shifting as we explore beyond the central nervous system, discovering that peripheral changes such as inflammatory dysfunctions may predict the rate of disease progression and severity. However, the cellular mechanisms driving these immunity changes remain largely unknown. Despite over 200 years of research on PD, robust diagnostic or progression biomarkers and disease altering therapeutics are still lacking. Thus, understanding peripheral immune signatures could lead to earlier diagnosis and more effective treatments for PD. Here, we sought to define the transcriptomic alterations of the complete peripheral immune cell compartment by single-cell RNA- and T-cell receptor-sequencing with hopes of uncovering PD signatures and potential peripheral blood biomarkers. Following transcriptional profiling of 78 876 cells from 10 healthy controls and 14 PD donors, we observed five major classes of immune cell types; myeloid (monocytes, dendritic cells) and lymphoid (T, B, natural killer) cells from which we identified 38 cellular subtypes following bioinformatic re-clustering. Comparing immune cell subtypes and phenotypes between PD patients and healthy controls revealed notable features of PD: 1) a significant shift of classical CD14+ monocytes towards an activated CD14+/CD83+ state, 2) changes in lymphocyte subtypes abundance, including a significant decrease in CD4+ naive and mucosal-associated invariant T-cells subtypes, along with an increase in CD56+ natural killer cells, 3) the identification by T-cell receptor sequencing of several PD specific T-cell clones shared between multiple patients, suggesting the implication of common epitopes in PD pathogenesis, 4) a notable increase in the expression of activation signature genes, including the AP-1 stress-response transcription factor complex, across all PD cell types. This signal was not present in atypical Parkinsonism patients with multiple systems atrophy or progressive supranuclear palsy. Overall, we present a comprehensive atlas of peripheral blood mononuclear cells from control and PD patients which should serve as a tool to improve our understanding of the role the immune cell landscape plays in PD pathogenesis.
帕金森病（PD）因其对中枢神经系统的影响而广为人知。最近的突破强调了中枢和外周系统之间的相互作用在帕金森病发病机制中的关键作用，凸显了帕金森病研究范式转变的必要性。我们发现，炎症功能障碍等外周变化可能预示着疾病的进展速度和严重程度。然而，驱动这些免疫变化的细胞机制在很大程度上仍不为人所知。尽管对帕金森病的研究已有 200 多年的历史，但目前仍缺乏强有力的诊断或病情进展生物标志物和改变病情的疗法。因此，了解外周免疫特征可能有助于更早地诊断和更有效地治疗帕金森病。在这里，我们试图通过单细胞 RNA 和 T 细胞受体测序来确定整个外周免疫细胞区的转录组变化，希望能发现帕金森病的特征和潜在的外周血生物标志物。在对来自 10 名健康对照组和 14 名帕金森病供体的 78 876 个细胞进行转录分析后，我们观察到了五大类免疫细胞类型：髓样细胞（单核细胞、树突状细胞）和淋巴细胞（T 细胞、B 细胞、自然杀伤细胞）。比较帕金森病患者和健康对照组的免疫细胞亚型和表型发现了帕金森病的显著特点：1）传统的 CD14+ 单核细胞明显转向活化的 CD14+/CD83+ 状态；2）淋巴细胞亚型丰度发生变化，包括 CD4+ 天真和粘膜相关不变 T 细胞亚型明显减少，CD56+ 自然杀伤细胞增加、3）通过 T 细胞受体测序鉴定出多个患者共有的几个 PD 特异性 T 细胞克隆，这表明在 PD 发病机制中存在共同的表位；4）在所有 PD 细胞类型中，包括 AP-1 应激反应转录因子复合物在内的激活标志基因的表达明显增加。这一信号在多系统萎缩或进行性核上性麻痹的非典型帕金森病患者中并不存在。总之，我们展示了对照组和帕金森病患者外周血单核细胞的综合图谱，该图谱可作为一种工具，帮助我们更好地了解免疫细胞在帕金森病发病机制中的作用。
{"title":"Mapping the peripheral immune landscape of Parkinson's disease patients with single-cell sequencing","authors":"Gael Moquin-Beaudry, Lovatiana Andriamboavonjy, Sebastien Audet, Laura Hamilton, Antoine Duquette, Sylvain Chouinard, Michel Panisset, Martine Tetreault","doi":"10.1101/2024.07.26.605020","DOIUrl":"https://doi.org/10.1101/2024.07.26.605020","url":null,"abstract":"Parkinson's Disease (PD) is widely recognized for its impact on the central nervous system. Recent breakthroughs underscore the crucial role of interactions between central and peripheral systems in PD's pathogenesis, highlighting the need for a paradigm shift in PD research. The spotlight is now shifting as we explore beyond the central nervous system, discovering that peripheral changes such as inflammatory dysfunctions may predict the rate of disease progression and severity. However, the cellular mechanisms driving these immunity changes remain largely unknown. Despite over 200 years of research on PD, robust diagnostic or progression biomarkers and disease altering therapeutics are still lacking. Thus, understanding peripheral immune signatures could lead to earlier diagnosis and more effective treatments for PD. Here, we sought to define the transcriptomic alterations of the complete peripheral immune cell compartment by single-cell RNA- and T-cell receptor-sequencing with hopes of uncovering PD signatures and potential peripheral blood biomarkers. Following transcriptional profiling of 78 876 cells from 10 healthy controls and 14 PD donors, we observed five major classes of immune cell types; myeloid (monocytes, dendritic cells) and lymphoid (T, B, natural killer) cells from which we identified 38 cellular subtypes following bioinformatic re-clustering. Comparing immune cell subtypes and phenotypes between PD patients and healthy controls revealed notable features of PD: 1) a significant shift of classical CD14+ monocytes towards an activated CD14+/CD83+ state, 2) changes in lymphocyte subtypes abundance, including a significant decrease in CD4+ naive and mucosal-associated invariant T-cells subtypes, along with an increase in CD56+ natural killer cells, 3) the identification by T-cell receptor sequencing of several PD specific T-cell clones shared between multiple patients, suggesting the implication of common epitopes in PD pathogenesis, 4) a notable increase in the expression of activation signature genes, including the AP-1 stress-response transcription factor complex, across all PD cell types. This signal was not present in atypical Parkinsonism patients with multiple systems atrophy or progressive supranuclear palsy. Overall, we present a comprehensive atlas of peripheral blood mononuclear cells from control and PD patients which should serve as a tool to improve our understanding of the role the immune cell landscape plays in PD pathogenesis.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862763","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 : 2024-07-27DOI: 10.1101/2024.07.27.605461
MD Mursalin Khan, Rita M. Graze
Sex dimorphism in immunity is commonly observed in a wide variety of taxa and is thought to arise from fundamental life history differences between females and males. In Drosophila melanogaster, infection with different pathogens typically results in different modes of immune sex dimorphism, with male- or female-bias, likely due to specific disease-causing mechanisms of pathogens and host-pathogen interactions. Studies showed that some pathways, such as IMD and Toll, can explain these sex-dimorphic immune responses in Drosophila. However, it is unclear if sex differences in the immune response observed in D. melanogaster are conserved, even in closely related species. One window into identifying conserved and evolving sex differences in the immune response is to examine the sex-differential expression of immunity-related genes. Here, we aim to understand whether two closely related species, D. melanogaster and D. simulans, show conserved sex dimorphism in innate immunity, focusing on associated changes in gene expression in response to infection with a gram-negative bacterium, Providencia rettgeri. Survival, bacterial load, and bacterial load upon death (BLUD) were investigated to assess overall sex differences. D. melanogaster females and males differed significantly in survival, whereas D. simulans did not. Enrichment analyses revealed that both sexes and species upregulate genes involved in similar immune-related biological processes, but downregulated groups differed. We identified conserved sex differential gene expression of genes in the bacterial infection response pathways IMD, Toll, Jak/STAT, their regulators, and other immune-related gene classes (e.g., BOMs), as well as sex and species differences. In D. melanogaster, the effector antimicrobial peptides (AMPs) regulated by IMD were more highly upregulated relative to D. simulans in both sexes. Moreover, D. melanogaster females uniquely initiated high levels of gene expression that were involved in negative feedback mechanisms that controlled the overstimulation of IMD. Genes in the Toll pathway were also sex-differentially expressed with a higher level of upregulation in D. melanogaster. Remarkably, comparing expression across species, we find that D. simulans likely employs both the conventional peptidoglycan recognition-driven PRR-SPE-Spz pathway and the microbial protease recognition-based Psh-dependent activation of Toll; in contrast, D. melanogaster appears to solely rely on the PRR-SPE-Spz pathway in this context. In summary, our findings indicate that sex differences are conserved in both species for the majority of upregulated genes, while downregulation patterns and specific gene subsets show notable differences between sexes or species.
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