Journal of Molecular Evolution最新文献_第4页

Exploring Structural Plastome Evolution in Asterales: Insights from Off-Target Hybrid Enrichment Data on the Small Single-Copy Region. 探索Asterales结构质体进化：来自小单拷贝区脱靶杂交富集数据的见解。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2024-12-26 DOI: 10.1007/s00239-024-10224-6

Adriana Benítez-Villaseñor, Matthias Jost, Carolina Granados Mendoza, Stefan Wanke, Rubi N Meza-Lázaro, Marcia Peñafiel Cevallos, Efraín Freire, Susana Magallón

{"title":"Exploring Structural Plastome Evolution in Asterales: Insights from Off-Target Hybrid Enrichment Data on the Small Single-Copy Region.","authors":"Adriana Benítez-Villaseñor, Matthias Jost, Carolina Granados Mendoza, Stefan Wanke, Rubi N Meza-Lázaro, Marcia Peñafiel Cevallos, Efraín Freire, Susana Magallón","doi":"10.1007/s00239-024-10224-6","DOIUrl":"10.1007/s00239-024-10224-6","url":null,"abstract":"The massive increase in the amount of plastid genome data have allowed researchers to address a variety of evolutionary questions within a wide range of plant groups. While plastome structure is generally conserved, some angiosperm lineages exhibit structural changes. Such is the case of the megadiverse order Asterales, where rearrangements in plastome structure have been documented. This study investigates the possibility of recovering plastid loci from off-target reads obtained through hybrid enrichment techniques. Our sampling includes 63 species from the eleven currently recognized families in Asterales derived from previously published studies. We assembled and annotated complete and partial plastomes using custom pipelines and estimate phylogenomic relationships. We retrieved plastid information from 60 of the 63 sampled species including a complete plastome from Tithonia tubaeformis (Asteraceae), circular partial (with gaps) plastomes from seven species, and non-circular partial plastomes from other 52 species. We focused on the small single-copy region because it could be recovered for over 29 species. Within the small single-copy region, we assessed intron losses and presence of putative pseudogenes. Comparative genomics revealed a relocated fragment of ~ 6500 bp in two Campanulaceae lineages (i. e. subfamily Lobelioideae and Pseudonemacladus oppositifolium), involving the genes rbcL, atpB, atpE, trnM-CAU, and trnV-UAC. Obtained phylogenetic hypotheses were congruent across the applied methods and consistent with previously published results. Our study demonstrates the feasibility of recovering plastid information, both complete and partial, from off-target hybrid enrichment data and provides insights on the structural plastome changes that have occurred throughout the evolution of the order Asterales.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"111-123"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations. 灵长类内源性逆转录病毒整合的2-LTR定年中的突变率变异和其他挑战。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2024-12-23 DOI: 10.1007/s00239-024-10225-5

Antoinette Cornelia van der Kuyl

{"title":"Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations.","authors":"Antoinette Cornelia van der Kuyl","doi":"10.1007/s00239-024-10225-5","DOIUrl":"10.1007/s00239-024-10225-5","url":null,"abstract":"The time of integration of germline-targeting Long Terminal Repeat (LTR) retroposons, such as endogenous retroviruses (ERVs), can be estimated by assessing the nucleotide divergence between the LTR sequences flanking the viral genes. Due to the viral replication mechanism, both LTRs are identical at the moment of integration, when the provirus becomes part of the host genome. After that time, proviral sequences evolve within the host DNA. When the mutation rate is known, nucleotide divergence between the LTRs would then be a measure of time elapsed since integration. Though frequently used, the approach has been complicated by the choice of host mutation rate and, to a lesser extent, by the method selected to estimate nucleotide divergence. As a result, outcomes can be incompatible with, for instance, speciation events identified from the fossil record. The review will give an overview of research reporting LTR-retroposon dating, and a summary of important factors to consider, including the quality, assembly, and alignment of sequences, the mutation rate of foreign DNA in host genomes, and the choice of a distance estimation method. Primates will here be the focus of the analysis because their genomes, ERVs, and fossil record have been extensively studied. However, most of the factors discussed have a wide applicability in the vertebrate field.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"62-82"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays. 更正：Fit-Seq2.0：一个改进的软件，用于高通量适应度测量使用池竞争分析。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 DOI: 10.1007/s00239-025-10232-0

Fangfei Li, Jason Tarkington, Gavin Sherlock

引用次数: 0

Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities. Id位点的共同祖先：染色体重排和多基因可能性。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2025-01-17 DOI: 10.1007/s00239-025-10233-z

Ashutosh Sharma, Nagarjun Vijay

{"title":"Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities.","authors":"Ashutosh Sharma, Nagarjun Vijay","doi":"10.1007/s00239-025-10233-z","DOIUrl":"10.1007/s00239-025-10233-z","url":null,"abstract":"The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the Id locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the Id locus, its precise location and functional details remain elusive. Our study aims to precisely locate the Id locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the Id locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the Id locus to a ~1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the Id locus shares a common ancestry across all BBC breeds, much like the Fm locus. Selection signatures and highly differentiated BBC-specific SNPs within the MTAP gene position it as the prime candidate for the Id locus with CCDC112 and additional genes, suggesting a possible polygenic nature. Our results suggest that the Id locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"163-180"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability. 正向选择塑造乳腺癌抑癌基因：揭示 BRCA1、BRCA2 和 MDC1 稳定性的奥秘。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2024-12-16 DOI: 10.1007/s00239-024-10222-8

Youssef M Fadel, Marwan Khaled, Mohamed Emam, Nour H Marzouk, Sief El-Din Sobih, Habiba Abd-Elaty, Wafaa M Elrashedy, Gehad Mostafa, Salma Alm Eldeen, Mohaned Bador, Agostinho Antunes, Mohamed El Hadidi

{"title":"Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability.","authors":"Youssef M Fadel, Marwan Khaled, Mohamed Emam, Nour H Marzouk, Sief El-Din Sobih, Habiba Abd-Elaty, Wafaa M Elrashedy, Gehad Mostafa, Salma Alm Eldeen, Mohaned Bador, Agostinho Antunes, Mohamed El Hadidi","doi":"10.1007/s00239-024-10222-8","DOIUrl":"10.1007/s00239-024-10222-8","url":null,"abstract":"Worldwide, breast cancer is the leading cause of death in women with cancers. Given this situation, new approaches to treatment are urgently needed. Tumor Suppressor Genes (TSGs) defects play a crucial role in tumor development, and recent studies propose their reactivation as a promising way for clinical intervention in breast cancer. Here, we performed detailed evolutionary analyses of 241 breast cancer TSGs across 25 mammalian genomes, revealing 28 genes under strong positive selection. These genes exhibit elevated molecular pressure in codons corresponding to amino acids located in crucial protein domains and motifs. Notably, one positively selected site in the BRCA1 C-terminal domain is known for its role in DNA damage response, suggesting potential interference with DNA repair mechanisms. Moreover, the substitution of some other sites found in important key motifs, namely two codons in BRCA2 (752 and 939) localized within the phosphoinositide-3-OH-kinase-related and playing a crucial role in the DNA repair and the DNA damage checkpoints. Our findings could be inspirational to foster future recommendations for drug-targeting sites and further illuminate the function of these proteins. Finally, the code developed in our study is delivered in the Automated tool for positive selection (ATPs) ( https://github.com/APS-P/Automated-Tool-for-Positive-Selection-ATPS-/wiki ) to assist the easy reproducibility and support future evolutionary genomics analyses.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"100-110"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142836947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

2024 Zuckerkandl Prize. “2024年糖Candl奖”。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-01-22 DOI: 10.1007/s00239-025-10234-y

Ugo Bastolla, Kerry Geiler-Samerotte, Maeva Perez, David A Liberles

引用次数: 0

Putative MutS2 Homologs in Algae: More Goods in Shopping Bag? 藻类中的推定 MutS2 同源物：购物袋里还有更多商品？

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-10-04 DOI: 10.1007/s00239-024-10210-y

Mariia Berdieva, Vera Kalinina, Olga Palii, Sergei Skarlato

{"title":"Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?","authors":"Mariia Berdieva, Vera Kalinina, Olga Palii, Sergei Skarlato","doi":"10.1007/s00239-024-10210-y","DOIUrl":"10.1007/s00239-024-10210-y","url":null,"abstract":"MutS2 proteins are presumably involved in either control of recombination or translation quality control in bacteria. MutS2 homologs have been found in plants and some algae; however, their actual diversity in eukaryotes remains unknown. We found putative MutS2 homologs in various species of photosynthetic eukaryotes and performed a detailed analysis of the revealed amino acid sequences. Three groups of homologs were distinguished depending on their domain composition: MutS2 homologs with full set of specific domains, MutS2-like sequences without endonuclease Smr domain, and MutS2-like homologs lacking Smr and clamp in domain IV, the extreme form of which are proteins with only a complete ATPase domain. We clarified the information about amino acid composition and set of specific motifs in the conserved domains in MutS2 and MutS2-like sequences. The models of the predicted tertiary structure were obtained for each group of homologs. The phylogenetic analysis demonstrated that all eukaryotic sequences split into two large groups. The first group included homologs belonging to species of Archaeplastida and a subset of haptophyte homologs, while the second-sequences of organisms from CASH groups (cryptophytes, alveolates, stramenopiles, haptophytes) and chlorarachniophytes. The cyanobacterial MutS2 clustered together with the first group, and proteins belonging to Deltaproteobacteria (orders Myxococcales and Bradymonadales) showed phylogenetic affinity to the CASH-including group with strong support. The observed tree pattern did not support a clear differentiation of eukaryotes into lineages with red and green algae-derived plastids. The results are discussed in the context of current conceptions of serial endosymbioses and genetic mosaicism in algae with complex plastids.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"815-833"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation. 冷活性脂肪酶（Glaciozyma antarctica PI12）的结构洞察：Alphafold2 预测与分子动力学模拟。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-16 DOI: 10.1007/s00239-024-10219-3

Adamu Idris Matinja, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Siti Nurbaya Oslan, Mohd Shukuri Mohamad Ali

{"title":"Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation.","authors":"Adamu Idris Matinja, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Siti Nurbaya Oslan, Mohd Shukuri Mohamad Ali","doi":"10.1007/s00239-024-10219-3","DOIUrl":"10.1007/s00239-024-10219-3","url":null,"abstract":"Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"944-963"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning. 分子进化原理：多层次学习理论的非平衡热力学概念》。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-08-29 DOI: 10.1007/s00239-024-10195-8

Jens Smiatek

引用次数: 0

Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli. 压力对大肠杆菌重要基因表达噪音的限制

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-10-11 DOI: 10.1007/s00239-024-10211-x

Perry A LaBoone, Raquel Assis

{"title":"Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli.","authors":"Perry A LaBoone, Raquel Assis","doi":"10.1007/s00239-024-10211-x","DOIUrl":"10.1007/s00239-024-10211-x","url":null,"abstract":"Gene expression is an inherently noisy process that is constrained by natural selection. Yet the condition dependence of constraint on expression noise remains unclear. Here, we address this problem by studying constraint on expression noise of E. coli genes in eight diverse growth conditions. In particular, we use variation in expression noise as an analog for constraint, examining its relationships to expression level and to the number of regulatory inputs from transcription factors across and within conditions. We show that variation in expression noise is negatively associated with expression level, implicating constraint to minimize expression noise of highly expressed genes. However, this relationship is condition dependent, with the strongest constraint observed when E. coli are grown in the presence of glycerol or ciprofloxacin, which result in carbon or antibiotic stress, respectively. In contrast, we do not observe evidence of constraint on expression noise of highly regulated genes, suggesting that highly expressed and highly regulated genes represent distinct classes of genes. Indeed, we find that essential genes are often highly expressed but not highly regulated, with elevated expression noise in glycerol and ciprofloxacin conditions. Thus, our findings support the hypothesis that selective constraint on expression noise is condition dependent in E. coli, illustrating how it may play a critical role in ensuring expression stability of essential genes in unstable environments.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"834-841"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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