Review
Plant Sciences
Yuanpeng Fang, Junmei Jiang, Xiaolong Hou, Jiyuan Guo, Xiangyang Li, Degang Zhao, Xin Xie
Summary: The evolution of gene families is crucial for understanding the evolutionary history and biodiversity of plants, as well as explaining their tolerance to environmental stresses. Studying the molecular evolution of plant gene families helps to gain insights into these important processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Pinar Onal, Himari Imaya Gunasinghe, Kristaley Yui Umezawa, Michael Zheng, Jia Ling, Leen Azeez, Anecine Dalmeus, Tasmima Tazin, Stephen Small
Summary: This study examines the evolution of the transcription factor Bicoid in fruit flies, showing that robust patterning activity of the Bcd HD is achieved only when amino acid substitutions in three separate subdomains are combined. Other combinations of subdomains also yield full rescue, but with lower penetrance, suggesting alternative suboptimal activities. These results suggest a multistep pathway for the evolution of the Bcd HD and demonstrate critical epistatic forces that contribute to the robust function of a DNA-binding domain.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Jonas Elsner, Martin A. Mensah, Manuel Holtgrewe, Jakob Hertzberg, Stefania Bigoni, Andreas Busche, Marie Coutelier, Deepthi C. de Silva, Nursel Elcioglu, Isabel Filges, Erica Gerkes, Katta M. Girisha, Luitgard Graul-Neumann, Aleksander Jamsheer, Peter Krawitz, Ingo Kurth, Susanne Markus, Andre Megarbane, Andre Reis, Miriam S. Reuter, Daniel Svoboda, Christopher Teller, Beyhan Tuysuz, Seval Turkmen, Meredith Wilson, Rixa Woitschach, Inga Vater, Almuth Caliebe, Wiebke Hulsemann, Denise Horn, Stefan Mundlos, Malte Spielmann
Summary: By conducting genome sequencing on 69 undiagnosed patients with congenital limb malformations, this study identified multiple potentially pathogenic genetic variants, including both known disease genes and novel disease genes. Additionally, complex structural variants were found, but no causative noncoding variants were identified.
Article
Entomology
Yan-Yan Zhou, Yue Jin, Shuai-Qi Liu, Shi-Liang Xu, Yu-Xin Huang, Yu-Song Xu, Lian-Gen Shi, Hua-Bing Wang
Summary: This study identified a lineage-specific expansion of lipocalin genes in lepidopteran insects, particularly in butterflies. Tandem duplication events played a role in this expansion, and some lipocalin genes involved in insect coloration underwent further expansion through tandem duplication. The study also revealed both conservation and divergence in the protein structures of lipocalins in lepidopteran insects. Expression analysis showed dynamic changes in tissue preference of lipocalin paralogs in Bombyx mori. Subcellular localization experiments demonstrated the localization of lipocalins in the cytoplasm, nuclear membrane, or nucleus in BmN cells. Furthermore, several lipocalin genes exhibited different responses to abiotic and biotic stresses.
Article
Plant Sciences
Hui Liu, Hai-Meng Lyu, Kaikai Zhu, Yves Van de Peer, Zong-Ming (Max) Cheng
Summary: This study identified multiple gene families in plant genomes containing intronless or intron-poor genes, which play important roles in response to drought and salt stress, epigenetic processes, and plant development. The origin, evolution, and potential functions of these intronless and intron-poor sub-families provide insights into plant genome evolution and gene functional divergence.
Article
Genetics & Heredity
Amber Harper, Luis Baudouin Gonzalez, Anna Schonauer, Ralf Janssen, Michael Seiter, Michaela Holzem, Saad Arif, Alistair P. McGregor, Lauren Sumner-Rooney
Summary: Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, and developmental genes such as homeobox genes and signaling pathway components are often retained as duplicates following WGD. In the arachnopulmonate lineage, similar patterns have been observed, providing evidence for ancestral WGD and potential insights into its evolutionary consequences. The study of embryonic transcriptomes and important gene families across multiple arachnopulmonate orders reveals consistent evolutionary trajectories within certain gene families across orders, but also interorder variation in the retention of specific paralogs. This comparative approach sheds light on the evolution of the developmental toolkit in arachnopulmonates and provides valuable transcriptomic data for future studies.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Amber Harper, Luis Baudouin Gonzalez, Anna Schonauer, Ralf Janssen, Michael Seiter, Michaela Holzem, Saad Arif, Alistair P. McGregor, Lauren Sumner-Rooney
Summary: Whole-genome duplications have occurred multiple times during animal evolution, resulting in new genetic material but also gene loss. Developmental genes are frequently retained as duplicates following these events, offering insights into evolutionary consequences. Studies in spiders and amblypygids are shedding light on the mechanisms of gene duplication and loss in arachnopulmonates.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemical Research Methods
Chaitanya Aluru, Mona Singh
Summary: The study introduces a reconciliation-based framework that considers the relative positions of protein domains within extant sequences to uncover tandem domain duplications accurately. By developing an integer linear programming approach and a heuristic algorithm, the researchers are able to identify single and tandem domain duplication events with high accuracy. Through extensive simulation studies and testing on an orthogroup with complex domain duplication patterns, the effectiveness of the approach is demonstrated.
Article
Marine & Freshwater Biology
Wenwu Yang, Zhixiong Deng, David Blair, Wei Hu, Mingbo Yin
Summary: The diversity and distribution of the freshwater rotifer Brachionus calyciflorus species complex were studied across China using molecular data. The results showed that this species complex was detected in 44 out of 251 waterbodies sampled, and it was categorized into four distinct species. Phylogenetic analysis based on mitochondrial and nuclear gene sequences revealed seven groups within the B. calyciflorus species complex in China. The occurrence of mito-nuclear discordance indicated occasional hybridization between different species of this complex.
Article
Multidisciplinary Sciences
Min Jiang, Peng Li, Wei Wang
Summary: The study revealed diverse MAPK and MKK genes in B. distachyon through systematic molecular evolutionary analysis, with MPK21-2 showing an exceptional evolutionary pattern, and functional divergences possibly occurring in MKK10 paralogues. Expression analysis also suggested that MAPKs and MKKs have different functions in various genetic contexts and under stress conditions.
Article
Biochemistry & Molecular Biology
Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O'Geen, Megan Y. Dennis
Summary: Evidence shows that in humans, paralogous segmental duplication genes exhibit different expression patterns, possibly due to relaxed selection or neofunctionalization. While ancestral paralogs show greater expression conservation with chimpanzee orthologs, certain derived paralogs may retain or supplant ancestral functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Yi Lei, Liandong Yang, Haifeng Jiang, Juan Chen, Ning Sun, Wenqi Lv, Shunping He
Summary: The study revealed that genome duplications in representative Cyprinidae fish facilitated phenotypic diversity in the Hb gene family, resulting in repeated evolutionary transitions and species-specific changes in gene content.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Jose Carlos Montanes, Marta Huertas, Xavier Messeguer, M. Mar Alba
Summary: The formation of new genes can occur through gene duplication or de novo formation from noncoding sequences. Both mechanisms show similarities in terms of low sequence constraints in the initial evolutionary stages, high turnover rates at the species level, and comparable persistence rates in deeper branches. Additionally, de novo proteins tend to have an excess of substitutions between charged amino acids, leading to rapid loss of their initial highly basic character.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Oncology
Sandrine M. Caputo, Dominique Telly, Adrien Briaux, Julie Sesen, Maurizio Ceppi, Francoise Bonnet, Violaine Bourdon, Florence Coulet, Laurent Castera, Capucine Delnatte, Agnes Hardouin, Sylvie Mazoyer, Ines Schultz, Nicolas Sevenet, Nancy Uhrhammer, Celine Bonnet, Anne-Francoise Tilkin-Mariame, Claude Houdayer, Virginie Moncoutier, Catherine Andrieu, Ivan Bieche, Marc-Henri Stern, Dominique Stoppa-Lyonnet, Rosette Lidereau, Christine Toulas, Etienne Rouleau
Summary: Large genomic rearrangements in BRCA1, such as deletions or duplications of one or multiple exons, are often found in the 5' region. Breakpoint localization helps understand chromatin structure in rearrangement-sensitive regions. Some rearrangement events are not necessarily harmful.
Article
Clinical Neurology
Li Yao, Zeyu Zhu, Chao Zhang, Wotu Tian, Li Cao
Summary: This study described three unrelated families with SPG2 caused by PLP1 mutations and summarized the genotype-phenotype correlations of PLP1-related cases worldwide. The study found that SPG2 caused by PLP1 mutations has significant clinical and genetic heterogeneity and is associated with white matter lesions and cognitive impairment.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Philip Donoghue, Jordi Paps
Article
Biochemistry & Molecular Biology
Alexander M. C. Bowles, Ulrike Bechtold, Jordi Paps
Article
Ecology
Cristina Guijarro-Clarke, Peter W. H. Holland, Jordi Paps
NATURE ECOLOGY & EVOLUTION
(2020)
Editorial Material
Biochemistry & Molecular Biology
Jordi Paps
Summary: The study discovered a shared genetic toolkit among many animals which regulates the transition to the juvenile form from an embryo or larva.
Article
Evolutionary Biology
Yichen Dai, Sonia Trigueros, Peter W. H. Holland
Summary: Gerbils are a subfamily of rodents living in arid regions of Asia and Africa. Recent studies have shown unusual amino acid changes in the PDX1 protein of several gerbil species, potentially affecting pancreatic development and beta-cell function, and these changes may be linked to a strong GC-bias in the genome. The evolutionary process of biased gene conversion may have pushed fixation of mutations adversely affecting function. These changes may not be entirely adaptive and could be associated with metabolic disorders in gerbil species on high carbohydrate diets.
JOURNAL OF MAMMALIAN EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Thomas D. Lewin, Amy H. Royall, Peter W. H. Holland
Summary: Most homeobox genes are conserved across animals, but ETCHbox genes in eutherians show dynamic patterns of gene loss and tandem duplication. Despite gene gain and loss, all sampled species have at least two ETCHbox genes, indicating their collective indispensable role. Evidence of positive selection and repeated gene conversion in TPRX1 and TPRX2 suggests these genes are dynamic in evolution with functional overlap and collective indispensable roles in mammalian species.
JOURNAL OF MOLECULAR EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Fei Xu, Ferdinand Marletaz, Daria Gavriouchkina, Xiao Liu, Tatjana Sauka-Spengler, Guofan Zhang, Peter W. H. Holland
Summary: The article discusses the similar expression patterns of Hox and ParaHox genes encoding transcription factors in divergent animals, highlighting the regulatory role of the Pdx gene on the insulin gene in Pacific oysters. The study shows that cgILP gene is co-expressed with cgPdx in oyster digestive tissue, indicating this gene interaction dates back to the origin of Bilateria.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Alexander M. C. Bowles, Jordi Paps, Ulrike Bechtold
Summary: Drought stress is a major constraint in crop production, with intense research being conducted on drought tolerance mechanisms for future production of drought tolerant crops. The variability in definitions of drought tolerance presents a challenge for systematic assessment across the plant kingdom. Drought tolerance is a polygenic trait, and understanding its evolution may provide insights into gene gain and loss patterns in relation to diverse drought adaptations.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Alexander M. C. Bowles, Jordi Paps, Ulrike Bechtold
Summary: By analyzing molecular data from 532 species, this study investigates the evolutionary origin and diversification of genes involved in the development and regulation of key adaptations to life in terrestrial environments. The results suggest that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history.
Article
Genetics & Heredity
Yang Zhang, Fan Mao, Shu Xiao, Haiyan Yu, Zhiming Xiang, Fei Xu, Jun Li, Lili Wang, Yuanyan Xiong, Mengqiu Chen, Yongbo Bao, Yuewen Deng, Quan Huo, Lvping Zhang, Wenguang Liu, Xuming Li, Haitao Ma, Yuehuan Zhang, Xiyu Mu, Min Liu, Hongkun Zheng, Nai-Kei Wong, Ziniu Yu
Summary: By sequencing the genome of C. hongkongensis and comparing it to other reference bivalve genomes, this study identified the genomic determinants driving the shift from byssal to cemented attachment in oysters. The loss of the Antennapedia gene and expansion of lineage-specific extracellular gene families were found to be implicated in this transition. Transcriptomic analysis revealed significant differences in gene expression profiles between the asymmetrical C. hongkongensis and the symmetrical P. fucata, including elevated expression of orthologous transcription factor genes and lineage-specific shell-related gene families.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Thomas D. Lewin, Ali A. Fouladi-Nashta, Peter W. H. Holland
Summary: This article investigates the role of ETCHbox genes in cattle and finds that ARGFX and LEUTX proteins can regulate the formation of blastocysts by upregulating genes normally expressed in blastocysts and downregulating genes associated with early development and undifferentiated cell state. The study also reveals overlapping functions of ARGFX and LEUTX in cattle, in contrast to their antagonistic roles in humans. Additionally, the research characterizes a mutant allele of ARGFX in cattle and shows that homozygous mutants are viable.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Peter O. Mulhair, Liam Crowley, Douglas H. Boyes, Amber Harper, Owen T. Lewis, Peter W. H. Holland
Summary: Homeobox genes encode transcription factors that play essential roles in the patterning and cell fate of developing animal embryos. Most Lepidoptera species have around 100 homeobox loci, including a unique Hox gene cluster. The Shx genes are generally conserved, but some moth lineages have undergone dramatic duplication in the Hox gene cluster.
Article
Evolutionary Biology
Thomas D. Lewin, Josephine R. Blagrove, Peter W. H. Holland
Summary: LEUTX is a homeodomain transcription factor that plays a role in embryonic genome activation. It is only found in eutherian mammals, including humans, but the encoded amino acid sequence differs greatly among mammalian species. This study reveals dramatic evolutionary sequence change in LEUTX within closely related primate species, suggesting rapid sequence evolution has fine-tuned its role within the primates.
GENOME BIOLOGY AND EVOLUTION
(2023)
Review
Ecology
Jordi Paps, Maria Eleonora Rossi, Alexander M. C. Bowles, Marta Alvarez-Presas
Summary: The Animal Kingdom, together with plants and fungi, is one of the three major lineages of multicellular eukaryotes. The origin and diversification of animals are crucial to modern evolutionary biology. Recent advancements in molecular biology and computational power have provided new insights into animal phylogenetics and genomics, complementing the findings from comparative morphology, evodevo, and palaeontology. This paper reviews the developments in these fields and compares animals to plants as another major lineage of multicellular eukaryotes.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)