Article
Agriculture, Multidisciplinary
Huang Yi-le, Zhang Ling-kui, Zhang Kang, Chen Shu-min, Hu Jian-bin, Cheng Feng
Summary: Whole genome duplication (WGD) and tandem duplication (TD) are important mechanisms in plant genome evolution. This study found that Vitis vinifera, which did not undergo a whole genome triplication event, retained more tandem duplicated gene (TDG) clusters compared to Solanaceae species that experienced the event. There was also a bias in the functional categories of genes retained through WGD and TD, with WGD retaining dose-sensitive genes and TD retaining stress resistance genes. The study also provided evidence of gene fusion events in TDG clusters, which contribute to functional innovation.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
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
Plant Sciences
Yanting Hu, Xiaopei Wu, Guihua Jin, Junchu Peng, Rong Leng, Ling Li, Daping Gui, Chuanzhu Fan, Chengjun Zhang
Summary: Thlaspi arvense, a plant thriving in extreme environments, has a genome dominated by LTR retrotransposons, particularly from the Gypsy superfamily. The expansion of LTR-RTs in the last six million years has contributed to the genome size increase in T. arvense. Genes flanked by LTRs show significant expansion and are involved in plant growth, development, and stress responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Mert Dogan, Milan Pouch, Terezie Mandakova, Petra Hlouskova, Xinyi Guo, Pieter Winter, Zuzana Chumova, Adriaan Van Niekerk, Klaus Mummenhoff, Ihsan A. Al-Shehbaz, Ladislav Mucina, Martin A. Lysak
Summary: The unigeneric tribe Heliophileae, which includes more than 100 Heliophila species, is morphologically diverse and endemic to southern Africa. Their evolution involves whole-genome duplication, diploidization, species radiations, and different ecological life histories. Despite the shared phylogenetic relationship between Chamira and Heliophila, they do not share tandem repeat sequences.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Immunology
Sheng Liu, Youli Liu, Jiali Lu, Jinxia Mao, Zhihua Lin, Qinggang Xue
Summary: This research identified 12 new members of the I84 protease inhibitor family in razor clams through genome-wide sequence analysis. These genes likely play a unique role in host defense in molluscs. The predicted mature peptides share common characteristics with previously reported family members. At the genomic level, these genes are organized into exons and introns, with many of them being tandemly duplicated. Additionally, differences in expression patterns were observed among the genes, with higher expression levels in Vibrio tolerant clams compared to non-tolerant ones.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Nomar Espinosa Waminal, Remnyl Joyce Pellerin, Sang-Ho Kang, Hyun Hee Kim
Summary: The study reveals the significant role of massive chromosomal rearrangements in shaping the unique dysploid karyotype of Senna tora by analyzing the composition and abundance of tandem repeats in its genome, and comparing their distribution with a closely related euploid species Senna occidentalis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Ophthalmology
Shijing Wu, Zhisheng Yuan, Zixi Sun, Tian Zhu, Xing Wei, Xuan Zou, Ruifang Sui
Summary: This study identified a novel large tandem duplication in the MCDR1 locus in a Chinese family with NCMD, showing a variety of macular phenotypes. The clinical features of the patients included macular involvement ranging from patchy lesions to big-area thinning, with BCVA ranging from 20/50 to 20/20, and varying degrees of macular structure disorganization observed on OCT.
GRAEFES ARCHIVE FOR CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY
(2022)
Review
Genetics & Heredity
Xi Zhang, David Roy Smith
Summary: This article provides a summary of research tools used for detecting gene duplicates, including metrics, computational approaches, and the latest developments in web tools and databases.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Akihiro Ezoe, Kazumasa Shirai, Kousuke Hanada
Summary: Gene duplication is a major mechanism for creating new genes in plants, resulting in duplicated genes with varying degrees of functional diversification. High diversified duplicates from tandem duplications tend to have lineage-specific functions, while low diversified duplicates from whole-genome duplications are related to essential signaling pathways, impacting plant evolution differently.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Marine & Freshwater Biology
Yu Wang, Yi Yang, Lingfeng Kong, Takenori Sasaki, Qi Li
Summary: In this study, the higher-level phylogeny of the Imparidentia superorder in Heterodonta was investigated by adding new mitochondrial sequences. The results provided a clearer understanding of the overall structure of the Imparidentia tree and the relationships among major lineages. Additionally, the molecular divergence times of nine nodes in the Imparidentia tree were inferred. Overall, this study contributes to a better-resolved phylogeny of Imparidentia based on mitochondrial genomes.
MARINE LIFE SCIENCE & TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Daria Kostiniuk, Hely Tamminen, Pashupati P. Mishra, Saara Marttila, Emma Raitoharju
Summary: The nc886 locus is not polymorphically imprinted in non-human primates and guinea pigs, unlike in humans, suggesting that animal models are not applicable for nc886 research. The data obtained suggests that the nc886 region may be classically imprinted in great apes and potentially also in Old World monkeys.
Article
Biochemistry & Molecular Biology
Manu Kumar Gundappa, Thu-Hien To, Lars Gronvold, Samuel A. M. Martin, Sigbjorn Lien, Juergen Geist, David Hazlerigg, Simen R. Sandve, Daniel J. Macqueen
Summary: This study investigates the long-term outcomes of autopolyploid rediploidization in salmonid fishes using genome-wide resolution. Analysis reveals an initial wave of rediploidization in the late Cretaceous followed by a period of genomic stasis and a second rediploidization wave in the early Eocene, coinciding with species diversification. Insights into potential functional outcomes of delayed rediploidization are provided through gene set enrichment, gene expression, and codon-based selection analyses. The study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
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
Ecology
Jose M. Martin-Duran, Bruno C. Vellutini, Ferdinand Marletaz, Viviana Cetrangolo, Nevena Cvetesic, Daniel Thiel, Simon Henriet, Xavier Grau-Bove, Allan M. Carrillo-Baltodano, Wenjia Gu, Alexandra Kerbl, Yamile Marquez, Nicolas Bekkouche, Daniel Chourrout, Jose Luis Gomez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol
Summary: This study presents the genome of the miniature segmented annelid Dimorphilus gyrociliatus, which shows no significant changes in genome structure and regulation compared to other cases of genome miniaturization. The research highlights a conservative route to genome compaction in annelids and sheds light on the causes and consequences of genome reduction in animals.
NATURE ECOLOGY & EVOLUTION
(2021)
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
Biology
Gustavo Sanchez, Fernando A. Fernandez-Alvarez, Morag Taite, Chikatoshi Sugimoto, Jeffrey Jolly, Oleg Simakov, Ferdinand Marletaz, Louise Allcock, Daniel S. Rokhsar
Summary: The study used genome sequencing and phylogenetic analysis to reveal the evolutionary relationships and divergence times of bobtail and bottletail squids, demonstrating their evolutionary process and diversification history. It was found that the ancestor of the Sepiolinae likely possessed a bilobed light organ with bacteriogenic luminescence, and analysis of divergence time suggested that major biogeographic events may have shaped the speciation of these animals.
COMMUNICATIONS BIOLOGY
(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
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
Multidisciplinary Sciences
Ksenia Skvortsova, Stephanie Bertrand, Danila Voronov, Paul E. Duckett, Samuel E. Ross, Marta Silvia Magri, Ignacio Maeso, Robert J. Weatheritt, Jose Luis Gomez Skarmeta, Maria Ina Arnone, Hector Escriva, Ozren Bogdanovic
Summary: The study shows that invertebrate deuterostomes use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes, indicating a conservation of this major gene-regulatory module in vertebrates.
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)
Article
Biotechnology & Applied Microbiology
Marina Braso-Vives, Ferdinand Marletaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, Jose L. Gomez-Skarmeta, Diego A. Hartasanchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia, Marc Robinson-Rechavi
Summary: The small-scale gene duplication history of amphioxus resembles that of vertebrates, despite their slower molecular and morphological evolution. Amphioxus gene duplicates show similar levels of expression and patterns of functional specialization as vertebrate duplicated genes.