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Genome Biology and Evolution

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https://read.qxmd.com/read/30778535/inter-and-intra-specific-transcriptional-and-phenotypic-responses-of-pseudo-nitzschia-under-different-nutrient-conditions
#1
Kimberley A Lema, Gabriel Metegnier, Julien Quéré, Marie Latimier, Agnès Youenou, Christophe Lambert, Juliette Fauchot, Mickael Le Gac
Untangling the functional basis of divergence between closely related species is a step towards understanding species dynamics within communities at both the evolutionary and ecological scales. We investigated cellular (i.e: growth, domoic acid production, nutrient consumption) and molecular (transcriptomic analyses) responses to varying nutrient concentrations across several strains belonging to three species of the toxic diatom genus Pseudo-nitzschia. Three main results were obtained. First, strains from the same species displayed similar transcriptomic, but not necessarily cellular, responses to the experimental conditions...
February 18, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30768172/integrative-genomics-reveals-the-genetics-and-evolution-of-the-honey-bee-s-social-immune-system
#2
Brock A Harpur, M Marta Guarna, Elizabeth Huxter, Heather Higo, Kyung-Mee Moon, Shelley E Hoover, Abdullah Ibrahim, Andony P Melathopoulos, Suresh Desai, Robert W Currie, Stephen F Pernal, Leonard J Foster, Amro Zayed
Social organisms combat pathogens through individual innate immune responses or through social immunity -allobehaviours that limit pathogen transmission within groups. While we have a relatively detailed understanding of the genetics and evolution of the innate immunity in animals, we know little about social immunity. Addressing this knowledge gap is crucial for understanding how life-history traits influence immunity, and if trade-offs exist between innate and social immunity. Hygienic behaviour in the Western honey bee, Apis mellifera, provides an excellent model for investigating the genetics and evolution of social immunity in animals...
February 15, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30753446/evolutionary-changes-after-translational-challenges-imposed-by-horizontal-gene-transfer
#3
Stéphanie Bedhomme, Dolors Amorós-Moya, Luz M Valero, Nùria Bonifaci, Miquel-Àngel Pujana, Ignacio G Bravo
Genes acquired by horizontal gene transfer (HGT) may provide the recipient organism with potentially new functions, but proper expression level and integration of the transferred genes in the novel environment are not granted. Notably, transferred genes can differ from the receiving genome in codon usage preferences (CUP), leading to impaired translation and reduced functionality.Here, we characterise the genomic and proteomic changes undergone during experimental evolution of Escherichia coli after HGT of three synonymous versions, presenting very different CUP, of an antibiotic resistance gene...
February 11, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30753430/multifarious-evolutionary-pathways-of-a-nuclear-rna-editing-factor-disjunctions-in-co-evolution-of-dot4-and-its-chloroplast-target-rpoc1eu488sl
#4
Anke Hein, Sarah Brenner, Volker Knoop
Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles co-evolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28 and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β' subunit mRNA...
February 11, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30753429/investigating-the-origins-of-membrane-phospholipid-biosynthesis-genes-using-outgroup-free-rooting
#5
Gareth A Coleman, Richard D Pancost, Tom A Williams
One of the key differences between Bacteria and Archaea are their canonical membrane phospholipids, which are synthesised by distinct biosynthetic pathways with non-homologous enzymes. This "lipid divide" has important implications for the early evolution of cells and the type of membrane phospholipids present in the last universal common ancestor (LUCA). One of the main challenges in studies of membrane evolution is that the key biosynthetic genes are ancient and their evolutionary histories are poorly resolved...
February 8, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30753418/analysis-of-the-functional-relevance-of-epigenetic-chromatin-marks-in-the-first-intron-associated-with-specific-gene-expression-patterns
#6
Shin-Sang Jo, Sun Shim Choi
We previously showed that the first intron of genes exhibits several interesting characteristics not seen in other introns: (1) it is the longest intron on average in almost all eukaryotes, (2) it presents the highest number of conserved sites, and (3) it exhibits the highest density of regulatory chromatin marks. Here, we expand on our previous study by integrating various multiomics data, leading to further evidence supporting the functionality of sites in the first intron. We first show that trait-associated single-nucleotide polymorphisms (TASs) are significantly enriched in the first intron...
February 8, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715360/the-tritryps-comparative-repeatome-insights-on-repetitive-element-evolution-in-trypanosomatid-pathogens
#7
Sebastián Pita, Florencia Díaz-Viraqué, Gregorio Iraola, Carlos Robello
The major human pathogens Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads...
February 4, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715356/whole-genome-sequence-data-uncover-widespread-heterothallism-in-a-largest-group-of-lichen-forming-fungi
#8
David Pizarro, Francesco Dal Grande, Steven D Leavitt, Paul S Dyer, Imke Schmitt, Ana Crespo, H Thorsten Lumbsch, Pradeep K Divakar
Fungal reproduction is regulated by the mating-type (MAT1) locus, which typically comprises two idiomorphic genes. The presence of one or both allelic variants at the locus determines the reproductive strategy in fungi - homothallism vs. heterothallism. It has been hypothesized that self-fertility via homothallism is widespread in lichen-forming fungi. To test this hypothesis, we characterized the MAT1 locus of 41 genomes of lichen-forming fungi representing a wide range of growth forms and reproductive strategies in the class Lecanoromycetes, the largest group of lichen-forming fungi...
February 4, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715341/evidence-of-austronesian-genetic-lineages-in-east-africa-and-south-arabia-complex-dispersal-from-madagascar-and-southeast-asia
#9
Nicolas Brucato, Veronica Fernandes, Pradiptajati Kusuma, Viktor Cerný, Connie J Mulligan, Pedro Soares, Terea Rito, Céline Besse, Anne Boland, Jean-Francois Deleuze, Murray P Cox, Herawati Sudoyo, Mark Stoneking, Luisa Pereira, François-Xavier Ricaut
The Austronesian dispersal across the Indonesian Ocean to Madagascar and the Comoros has been well documented, but in an unexplained anomaly, few to no traces have been found of the Austronesian expansion in East Africa or the Arabian Peninsula. To revisit this peculiarity, we surveyed the Western Indian Ocean rim populations to identify potential Austronesian genetic ancestry. We generated full mtDNA genomes and genome-wide genotyping data for these individuals and compared them with the Banjar, the Indonesian source population of the westward Austronesian dispersal...
February 4, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715330/extensive-reduction-of-the-nuclear-pore-complex-in-nucleomorphs
#10
Nicholas A T Irwin, Patrick J Keeling
The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved amongst eukaryotes. Potential exceptions to this are nucleomorphs: highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans...
February 4, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715343/genome-analysis-of-shigella-flexneri-serotype-3b-strain-sfl1520-reveals-significant-horizontal-gene-acquisitions-including-a-multidrug-resistance-cassette
#11
Pawan Parajuli, Lachlan P Deimel, Naresh K Verma
Shigella flexneri is a major etiological agent of shigellosis in developing countries, primarily occurring in children under five years of age. We have sequenced, for the first time, the complete genome of S. flexneri serotype 3b (strain SFL1520). We used a hybrid sequencing method--both long-read MinION Flow (Oxford Nanopore Technologies) and short-read MiSeq (Illumina) sequencing to generate a high-quality reference genome. The SFL1520 chromosome was found to be approximately 4.58 Mb long, with 4,729 coding sequences (CDS)...
February 1, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715337/complete-genome-sequence-of-the-wolbachia-walbb-endosymbiont-of-aedes-albopictus
#12
Amit Sinha, Zhiru Li, Luo Sun, Clotilde K S Carlow
Wolbachia, an alpha-proteobacterium closely related to Rickettsia, is a maternally transmitted, intracellular symbiont of arthropods and nematodes. Aedes albopictus mosquitoes are naturally infected with Wolbachia strains wAlbA and wAlbB. Cell line Aa23 established from Ae. albopictus embryos retains only wAlbB and is a key model to study host-endosymbiont interactions. We have assembled the complete circular genome of wAlbB from the Aa23 cell line using long-read PacBio sequencing at 500X median coverage. The assembled circular chromosome is 1...
February 1, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715335/extensive-losses-of-photosynthesis-genes-in-the-plastome-of-a-mycoheterotrophic-orchid-cyrtosia-septentrionalis-vanilloideae-orchidaceae
#13
Young-Kee Kim, Sangjin Jo, Se-Hwan Cheon, Min-Jung Joo, Ja-Ram Hong, Myoung Hai Kwak, Ki-Joong Kim
Cyrtosia septentrionalis is an achlorophyllous mycoheterotrophic orchid in the subfamily Vanilloideae (Orchidaceae). This paper reports C. septentrionalis' complete plastome sequence and compare it to other orchid plastomes with a same mycoheterotrophic nutritional mode. The C. septentrionalis plastome has decreased to 96,859 bp in length, but it still maintains a quadripartite structure. The C. septentrionalis plastome contains 38 protein-coding genes, 25 tRNA genes, and four ribosomal RNA genes. Most genes related to photosynthesis have been lost, whereas the majority of housekeeping genes remain; this pattern corresponds to the end of stage 3 gene degradation...
February 1, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30715331/demographic-history-of-the-human-commensal-drosophila-melanogaster
#14
J Roman Arguello, Stefan Laurent, Andrew G Clark
The cohabitation of Drosophila melanogaster with humans is nearly ubiquitous. Though it has been well-established that this fly species originated in sub-Saharan Africa, and only recently has spread globally, many details of its swift expansion remain unclear. Elucidating the demographic history of D. melanogaster provides a unique opportunity to investigate how human movement might have impacted patterns of genetic diversity in a commensal species, as well as providing neutral null models for studies aimed at identifying genomic signatures of local adaptation...
January 31, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30698789/pdz-domains-across-the-microbial-world-molecular-link-to-the-proteases-stress-response-and-protein-synthesis
#15
Vijaykumar Yogesh Muley, Yusuf Akhter, Sanjeev Galande
The PSD-95/Dlg-A/ZO-1 (PDZ) domain is highly expanded, diversified and well distributed across the metazoa where it assembles diverse signalling components by virtue of interactions with other proteins in a sequence-specific manner. In contrast, in the microbial world they are reported to be involved in protein quality control during stress response. The distribution, functions, and origins of PDZ domain-containing proteins in the prokaryotic organisms remain largely unexplored. We analysed 7,852 PDZ domain-containing proteins in 1,474 microbial genomes in this context...
January 29, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30698765/identification-of-cell-death-genes-in-sea-urchin-paracentrotus-lividus-and-their-expression-patterns-during-embryonic-development
#16
C Galasso, S D'Aniello, C Sansone, A Ianora, G Romano
Apoptosis and autophagy are fundamental mechanisms of Programmed Cell Death (PCD) activated during protostome and deuterostome embryonic development, contributing to the creation and remodelling of different anatomical structures. PCD has been investigated at morphological and biochemical level, but there is a lack of information concerning gene expression of death factors during deuterostome embryonic development. In this study, we analyse the expression patterns of 13 genes involved in autophagy, extrinsic and intrinsic apoptosis during blastula, gastrula and pluteus stages of the sea urchin Paracentrotus lividus embryonic development...
January 29, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30698705/jmjc-domain-encoding-genes-are-conserved-in-highly-regenerative-metazoans-and-are-associated-with-planarian-whole-body-regeneration
#17
Ping-Lin Cao, Nobuyoshi Kumagai, Takeshi Inoue, Kiyokazu Agata, Takashi Makino
The capacity for regeneration varies greatly among metazoans, yet little is known about the evolutionary processes leading to such different regeneration abilities. In particular, highly regenerative species such as planarians and cnidarians can regenerate the whole body from an amputated fragment; however, a common molecular basis, if any, among these species remains unclear. Here, we show that genes encoding Jumonji C (JmjC) domain-containing proteins are associated with high regeneration ability. We classified 132 fully sequenced metazoans into two groups with high or low regeneration abilities and identified 118 genes conserved in the high regenerative group that were lost in species in the low-regeneration group during evolution...
January 29, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30689862/small-segmental-duplications-in-drosophila-high-rate-of-emergence-and-elimination
#18
Juan Li, Lan Jiang, Chung-I Wu, Xuemei Lu, Shu Fang, Chau-Ti Ting
Segmental duplications are an important class of mutations. Because a large proportion of segmental duplications may often be strongly deleterious, high frequency or fixed segmental duplications may represent only a tiny fraction of the mutational input. To understand the emergence and elimination of segmental duplications, we survey polymorphic duplications, including tandem and interspersed duplications, in natural populations of Drosophila by haploid embryo genomes. As haploid embryos are not expected to be heterozygous the genome, sites of heterozygosity (referred to as pseudoheterozygous sites, or PHS), may likely represent recent duplications that have acquired new mutations...
January 28, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30689841/exome-re-sequencing-reveals-evolutionary-history-genomic-diversity-and-targets-of-selection-in-the-conifers-pinus-taeda-and-pinus-elliottii
#19
Juan J Acosta, Annette M Fahrenkrog, Leandro G Neves, Márcio F R Resende, Christopher Dervinis, John M Davis, Jason A Holliday, Matias Kirst
Loblolly pine (Pinus taeda) and slash pine (Pinus elliottii) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, while none are available for P. elliottii. Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P...
January 28, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30689829/evolution-of-the-d-melanogaster-chromatin-landscape-and-its-associated-proteins
#20
Elise Parey, Anton Crombach
In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types were given colour names in reference to the Greek word chroma. They are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing, and histone modifications...
January 28, 2019: Genome Biology and Evolution
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