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Allopolyploid subgenome identification and implications for evolutionary analysis 异源多倍体亚基因组鉴定及其对进化分析的影响
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-17 DOI: 10.1016/j.tig.2024.03.008
Adam M. Session
{"title":"Allopolyploid subgenome identification and implications for evolutionary analysis","authors":"Adam M. Session","doi":"10.1016/j.tig.2024.03.008","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.008","url":null,"abstract":"<p>Whole-genome duplications (WGDs) are widespread genomic events in eukaryotes that are hypothesized to contribute to the evolutionary success of many lineages, including flowering plants, <em>Saccharomyces</em> yeast, and vertebrates. WGDs generally can be classified into autopolyploids (ploidy increase descended from one species) or allopolyploids (ploidy increase descended from multiple species). Assignment of allopolyploid progenitor species (called subgenomes in the polyploid) is important to understanding the biology and evolution of polyploids, including the asymmetric subgenome evolution following hybridization (biased fractionation). Here, I review the different methodologies used to identify the ancestors of allopolyploid subgenomes, discuss the advantages and disadvantages of these methods, and outline the implications of how these methods affect the subsequent evolutionary analysis of these genomes.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140629310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The role of omics in improving the orphan crop tef 奥米克斯技术在改良孤儿作物柚子中的作用
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-09 DOI: 10.1016/j.tig.2024.03.003
Lorena Y. Ramírez Gonzales, Gina Cannarozzi, Lea Jäggi, Kebebew Assefa, Solomon Chanyalew, Matteo Dell’Acqua, Zerihun Tadele
{"title":"The role of omics in improving the orphan crop tef","authors":"Lorena Y. Ramírez Gonzales, Gina Cannarozzi, Lea Jäggi, Kebebew Assefa, Solomon Chanyalew, Matteo Dell’Acqua, Zerihun Tadele","doi":"10.1016/j.tig.2024.03.003","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.003","url":null,"abstract":"<p>Tef or teff [<em>Eragrostis tef</em> (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef’s diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140629306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Subscription and Copyright Information 订阅和版权信息
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-08 DOI: 10.1016/s0168-9525(24)00059-3
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/s0168-9525(24)00059-3","DOIUrl":"https://doi.org/10.1016/s0168-9525(24)00059-3","url":null,"abstract":"Abstract not available","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advisory Board and Contents 咨询委员会和内容
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-08 DOI: 10.1016/s0168-9525(24)00056-8
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/s0168-9525(24)00056-8","DOIUrl":"https://doi.org/10.1016/s0168-9525(24)00056-8","url":null,"abstract":"Abstract not available","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Diverse pathways to speciation revealed by marine snails. 海洋蜗牛揭示了物种形成的多种途径。
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-01 Epub Date: 2024-02-22 DOI: 10.1016/j.tig.2024.01.002
Kerstin Johannesson, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja Marie Westram, Roger K Butlin, Sean Stankowski
{"title":"Diverse pathways to speciation revealed by marine snails.","authors":"Kerstin Johannesson, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja Marie Westram, Roger K Butlin, Sean Stankowski","doi":"10.1016/j.tig.2024.01.002","DOIUrl":"10.1016/j.tig.2024.01.002","url":null,"abstract":"<p><p>Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139941244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Force-free activation of Notch with DNA origami. 利用 DNA 折纸无力激活 Notch。
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-01 Epub Date: 2024-03-15 DOI: 10.1016/j.tig.2024.03.001
Hyun Min Kim, Mark Bathe
{"title":"Force-free activation of Notch with DNA origami.","authors":"Hyun Min Kim, Mark Bathe","doi":"10.1016/j.tig.2024.03.001","DOIUrl":"10.1016/j.tig.2024.03.001","url":null,"abstract":"<p><p>The Notch signaling pathway is a highly conserved, fundamental process to embryogenesis and neurogenesis. While force-induced conformational change is known to activate Notch receptors, Smyrlaki et al. recently used DNA origami to reveal an additional, force-independent mode of Notch activation via soluble presentation of spatially controlled ligand nanopatterns.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140141107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges. 将 RNA 修改机制引向内源性 RNA：机遇与挑战。
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-01 Epub Date: 2024-02-12 DOI: 10.1016/j.tig.2024.01.001
Monika Witzenberger, Schraga Schwartz
{"title":"Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges.","authors":"Monika Witzenberger, Schraga Schwartz","doi":"10.1016/j.tig.2024.01.001","DOIUrl":"10.1016/j.tig.2024.01.001","url":null,"abstract":"<p><p>Over 170 chemical modifications can be naturally installed on RNA, all of which are catalyzed by dedicated machineries. These modifications can alter RNA sequence structure, stability, and translation as well as serving as quality control marks that record aspects of RNA processing. The diverse roles played by RNAs within cells has motivated endeavors to exogenously introduce RNA modifications at target sites for diverse purposes ranging from recording RNA:protein interactions to therapeutic applications. Here, we discuss these applications and the approaches that have been employed to engineer RNA-modifying machineries, and highlight persisting challenges and perspectives.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139730972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Architecture of an RNA polymerase ribozyme illuminates the RNA World. RNA 聚合酶核糖酶的结构照亮了 RNA 世界。
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-01 Epub Date: 2024-03-13 DOI: 10.1016/j.tig.2024.02.008
David M Shechner
{"title":"Architecture of an RNA polymerase ribozyme illuminates the RNA World.","authors":"David M Shechner","doi":"10.1016/j.tig.2024.02.008","DOIUrl":"10.1016/j.tig.2024.02.008","url":null,"abstract":"<p><p>'Ribo-organisms' of the primordial RNA World would have needed ribozymes that catalyze RNA replication. McRae, Wan, Kristoffersen et al. recently revealed how these RNA replicases might have functioned by solving the structure of an artificial polymerase ribozyme. This work illustrates how complex RNA structures evolve, with implications for the origins of life.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11003837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140133258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dominance and multi-locus interaction. 优势和多基因相互作用
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-01 Epub Date: 2024-03-07 DOI: 10.1016/j.tig.2023.12.003
Juan Li, Claudia Bank
{"title":"Dominance and multi-locus interaction.","authors":"Juan Li, Claudia Bank","doi":"10.1016/j.tig.2023.12.003","DOIUrl":"10.1016/j.tig.2023.12.003","url":null,"abstract":"<p><p>Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with the genetic background of the focal locus. Here, alleles at other loci modify the observed phenotype through position effects or dominance modifiers that are sometimes associated with pathogen resistance, lineage, sex, or mating type. Theoretical models have illustrated how variable dominance appears in the context of multi-locus interaction (epistasis). Here, we review empirical evidence for variable dominance and how the observed patterns may be captured by proposed epistatic models. We highlight how integrating epistasis and dominance is crucial for comprehensively understanding adaptation and speciation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140061305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Time is ticking faster for long genes in aging. 衰老长基因的时间在加速流逝。
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-01 Epub Date: 2024-03-21 DOI: 10.1016/j.tig.2024.01.009
Sourena Soheili-Nezhad, Olga Ibáñez-Solé, Ander Izeta, Jan H J Hoeijmakers, Thomas Stoeger
{"title":"Time is ticking faster for long genes in aging.","authors":"Sourena Soheili-Nezhad, Olga Ibáñez-Solé, Ander Izeta, Jan H J Hoeijmakers, Thomas Stoeger","doi":"10.1016/j.tig.2024.01.009","DOIUrl":"10.1016/j.tig.2024.01.009","url":null,"abstract":"<p><p>Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11003850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140190335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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