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Genome Biology and Evolution

Zi-Wen Li, Xing-Hui Hou, Jia-Fu Chen, Yong-Chao Xu, Qiong Wu, Josefa González, Ya-Long Guo
Transposable elements (TEs) are mobile genetic elements with very high mutation rates that play important roles in shaping genome architecture and regulating phenotypic variation. However, the extent to which TEs influence the adaptation of organisms in their natural habitats is largely unknown. Here, we scanned 201 representative re-sequenced genomes from the model plant Arabidopsis thaliana and identified 2,311 polymorphic TEs from non-centromeric regions. We found expansion and contraction of different types of TEs in different A...
August 9, 2018: Genome Biology and Evolution
Michael Brauchle, Adem Bilican, Claudia Eyer, Xavier Bailly, Pedro Martínez, Peter Ladurner, Rémy Bruggmann, Simon G Sprecher
Homeodomain transcription factors are involved in many developmental processes across animals and have been linked to body plan evolution. Detailed classifications of these proteins identified 11 distinct classes of homeodomain proteins in animal genomes, each harboring specific sequence composition and protein domains. While humans contain the full set of classes, D. melanogaster and C. elegans each lack one specific class. Furthermore, representative previous analyses in sponges, ctenophores and cnidarians could not identify several classes in those non-bilaterian metazoan taxa...
August 8, 2018: Genome Biology and Evolution
Wen-Sui Lo, Gail E Gasparich, Chih-Horng Kuo
Convergent evolution, a process by which organisms evolved independently to have similar traits, provides opportunities to understand adaptation. The bacterial genus Mycoplasma contains multiple species that evolved independently to become ruminant pathogens, which represents an interesting study system for investigating the process. In this work, we determined the genome sequences of 11 Entomoplasma/Mesoplasma species. This new data set, together with the other available Mollicutes genomes, provided comprehensive taxon sampling for inferring the gene content evolution that led to the emergence of Mycoplasma Mycoides cluster...
August 8, 2018: Genome Biology and Evolution
Hager Gaouda, Takashi Hamaji, Kayoko Yamamoto, Hiroko Kawai-Toyooka, Masahiro Suzuki, Hideki Noguchi, Yohei Minakuchi, Atsushi Toyoda, Asao Fujiyama, Hisayoshi Nozaki, David Roy Smith
Plastid genomes are not normally celebrated for being large. But researchers are steadily uncovering algal lineages with big and, in rare cases, enormous plastid DNAs (ptDNAs), such as volvocine green algae. Plastome sequencing of five different volvocine species has revealed some of the largest, most repeat-dense plastomes on record, including that of Volvox carteri  (∼525 kb). Volvocine algae have also been used as models for testing leading hypotheses on organelle genome evolution (e.g., the mutational hazard hypothesis), and it has been suggested that ptDNA inflation within this group might be a consequence of low mutation rates and/or the transition from a unicellular to multicellular existence...
August 8, 2018: Genome Biology and Evolution
Natalia Westervelt, Brian P Chadwick
Appreciation is growing for how chromosomes are organized in three-dimensional space at interphase. Microscopic and high throughput sequence-based studies have established that the mammalian inactive X chromosome (Xi) adopts an alternate conformation relative to the active X chromosome. The Xi is organized into several multi-megabase chromatin loops called superloops. At the base of these loops are superloop anchors, and in humans three of these anchors are composed of large tandem repeat DNA that include DXZ4, FIRRE and ICCE...
August 8, 2018: Genome Biology and Evolution
Homa Papoli Yazdi, Hans Ellegren
Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae...
August 7, 2018: Genome Biology and Evolution
C Grosche, A Diehl, S A Rensing, U G Maier
Plastids surrounded by four membranes harbour a special compartment between the outer and inner plastid membrane pair, the so-called periplastidal compartment (PPC). This cellular structure is usually presumed to be the reduced cytoplasm of a eukaryotic phototrophic endosymbiont, which was integrated into a host cell and streamlined into a plastid with a complex membrane structure. Up to date, no mitochondrion or mitochondrion-related organelle has been identified in the PPC of any representative. However, two prominent groups, the cryptophytes and the chlorarachniophytes, still harbour a reduced cell nucleus of symbiont origin, the nucleomorph, in their PPCs...
August 2, 2018: Genome Biology and Evolution
Guang-Ming Shao, Xi-Yin Li, Yang Wang, Zhong-Wei Wang, Zhi Li, Xiao-Juan Zhang, Li Zhou, Jian-Fang Gui
Allopolyploidization plays an important role in speciation and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid animals is scarce. In this study, the genome constitution and DNA methylation inheritance in a newly synthetic allopolyploid of gynogenetic gibel carp were analyzed. The incorporation of a whole genome of paternal common carp sperm in the allopolyploid was confirmed by genomic in situ hybridization (GISH), chromosome localization of 45S rDNAs and sequence comparison...
August 2, 2018: Genome Biology and Evolution
Bryan A Moyers, Jianzhi Zhang
Phylostratigraphy is a method for estimating gene age, usually applied to large numbers of genes in order to detect nonrandom age-distributions of gene properties that could shed light on mechanisms of gene origination and evolution. However, phylostratigraphy underestimates gene age with a non-negligible probability. The underestimation is severer for genes with certain properties, creating spurious age distributions of these properties and those correlated with these properties. Here we explore three strategies to reduce phylostratigraphic error/bias...
July 30, 2018: Genome Biology and Evolution
Jouni Kvist, Camila Gonçalves Athanàsio, Omid Shams Solari, James B Brown, John K Colbourne, Michael E Pfrender, Leda Mirbahai
DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here we explore the DNA methylation profile of two species of the crustacean Daphnia using whole genome bisulfite sequencing. We then compare our data with the methylomes of two insects and two mammals to achieve a better understanding of the function of DNA methylation in Daphnia...
July 30, 2018: Genome Biology and Evolution
Carolina Río Bártulos, Matthew B Rogers, Tom A Williams, Eleni Gentekaki, Henner Brinkmann, Rüdiger Cerff, Marie-Françoise Liaud, Adrian B Hehl, Nigel R Yarlett, Ansgar Gruber, Peter G Kroth, Mark van der Giezen
The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host...
July 30, 2018: Genome Biology and Evolution
Wen Wei, Lifeng Xiong, Yuan-Nong Ye, Meng-Ze Du, Yi-Zhou Gao, Kai-Yue Zhang, Yan-Ting Jin, Zujun Yang, Po-Chun Wong, Susanna K P Lau, Biao Kan, Jun Zhu, Patrick C Y Woo, Feng-Biao Guo
Pandemic cholera is a major concern for public health because of its high mortality and morbidity. Mutation accumulation (MA) experiments were performed on a representative strain of the current cholera pandemic. Although the base-pair substitution mutation rates in Vibrio cholerae (1.24×10-10 per site per generation for wild-type lines and 3.29 × 10-8 for mismatch repair deficient lines) are lower than that previously reported in other bacteria using MA analysis, we discovered specific high rates (8.31 × 10-8 site/generation for wild-type lines and 1...
July 30, 2018: Genome Biology and Evolution
Anna Allué-Guardia, Sara S K Koenig, Pablo Quirós, Maite Muniesa, James L Bono, Mark Eppinger
Shigella sonnei is responsible for the majority of shigellosis infections in the United States with over 500,000 cases reported annually. Here we present the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophage infections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termed p866, confers resistance to five different classes of antibiotics including ß-lactamase, sulphonamide, tetracycline, aminoglycoside, and trimethoprim...
July 30, 2018: Genome Biology and Evolution
Samuel Abalde, Manuel J Tenorio, Carlos M L Afonso, Rafael Zardoya
The transcriptome of the venom duct of the Atlantic piscivorous cone species Chelyconus ermineus (Born 1778) was determined. The venom repertoire of this species includes at least 378 conotoxin precursors, which could be ascribed to 33 known and 22 new (unassigned) protein superfamilies, respectively. Most abundant superfamilies were T, W, O1, M, O2, and Z, accounting for 57% of all detected diversity. A total of three individuals were sequenced showing considerable intraspecific variation: each individual had many exclusive conotoxin precursors, and only 20% of all inferred mature peptides were common to all individuals...
July 30, 2018: Genome Biology and Evolution
Ramesh R Vetukuri, Sucheta Tripathy, Mathu Malar C, Arijit Panda, Sandeep K Kushwaha, Aakash Chawade, Erik Andreasson, Laura J Grenville-Briggs, Stephen C Whisson
Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. Compared to other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organised in 1919 contigs and 1898 scaffolds, encompassing 11741 predicted genes, and has a repeat content of approximately 15%...
July 30, 2018: Genome Biology and Evolution
Blair W Perry, Daren C Card, Joel W McGlothlin, Giulia I M Pasquesi, Richard H Adams, Drew R Schield, Nicole R Hales, Andrew B Corbin, Jeffery P Demuth, Federico G Hoffmann, Michael W Vandewege, Ryan K Schott, Nihar Bhattacharyya, Belinda S W Chang, Nicholas R Casewell, Gareth Whiteley, Jacobo Reyes-Velasco, Stephen P Mackessy, Kenneth B Storey, Kyle K Biggar, Courtney N Passow, Chih-Horng Kuo, Suzanne E McGaugh, Anne M Bronikowski, Jason de Koning, Scott V Edwards, Michael E Pfrender, Patrick Minx, Edmund D Brodie, Edmund D Brodie, Wesley C Warren, Todd A Castoe
Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes...
July 30, 2018: Genome Biology and Evolution
Alina Minias, Piotr Minias, Bozena Czubat, Jaroslaw Dziadek
Mycobacterium tuberculosis is one of the deadliest and most challenging pathogens to study in current microbiological research. One of the issues that remains to be resolved is the importance of cobalamin in the metabolism of M. tuberculosis. The functionality of a vitamin B12 biosynthesis pathway in M. tuberculosis is under dispute, and the ability of this pathogen to scavenge vitamin B12 from the host is unknown. Here, we quantified the ratios of non-synonymous and synonymous nucleotide substitution rates (dN/dS) in the genes involved in vitamin B12 biosynthesis and transport and in genes encoding cobalamin-dependent enzymes in nearly four thousand strains of M...
July 30, 2018: Genome Biology and Evolution
Xinzhu Wei, Jianzhi Zhang
Ribosomes are highly abundant in cells and comprise, besides RNAs of varying lengths, 55-80 similarly sized, short proteins. This seemingly unusual composition is thought to have resulted from selection for rapid autocatalytic ribosome production. Here we demonstrate that ribosomal protein-splitting mutations cannot accelerate ribosome production. The autocatalytic explanation is also unnecessary, because protein lengths generally decline with expression levels. Although ribosomal proteins are shorter than expected from their expression levels, they are not outliers among members of large protein complexes in mean protein length or coefficient of variation...
July 30, 2018: Genome Biology and Evolution
Suresh Panthee, Hiroshi Hamamoto, Sanae A Ishijima, Atmika Paudel, Kazuhisa Sekimizu
Candida albicans TIMM1768 is a highly virulent strain utilized as a model organism for the study of gastrointestinal and oral candidiasis. Despite being a model strain, identification of its genetic determinants of pathogenesis is hindered by the unavailability of its genome sequence. In this study, we determined the genome sequence of C. albicans TIMM1768 using reads obtained from portable MinION and benchtop Ion PGM sequencers. Genome annotation and a comparative analysis with published genomes revealed that the TIMM1768 strain was close to Candida albicans CHN1, and we identified a significant number of genes encoding for pathogenesis...
July 30, 2018: Genome Biology and Evolution
Stefano Berto, Katja Nowick
The human prefrontal cortex (PFC) differs from that of other primates with respect to size, histology, and functional abilities. Here we analyzed genome wide expression data of humans, chimpanzees, and rhesus macaques to discover evolutionary changes in transcription factor (TF) networks that may underlie these phenotypic differences. We determined the co-expression networks of all TFs with species-specific expression including their potential target genes and interaction partners in the PFC of all three species...
July 30, 2018: Genome Biology and Evolution
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