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Genome Biology and Evolution

Alison S Jacob, Lee O'Brien Andersen, Paulina Pavinski Bitar, Vincent P Richards, Sarah Shah, Michael J Stanhope, C Rune Stensvold, C Graham Clark
Complete mitochondrion-related organelle (MRO) genomes of several subtypes (STs) of the unicellular stramenopile Blastocystis are presented. Complete conservation of gene content and synteny in gene order is observed across all MRO genomes, comprising 27 protein coding genes, 2 ribosomal RNA genes and 16 transfer RNA (tRNA) genes. Despite the synteny, differences in the degree of overlap between genes was observed between subtypes and also between isolates within the same subtype. Other notable features include unusual base-pairing mismatches in the predicted secondary structures of some tRNAs...
November 3, 2016: Genome Biology and Evolution
Florian Maumus, Guillaume Blanc
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain unicellular eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. These findings prompted us to search the genome of Acanthamoeba castellanii strain Neff (Neff), one of the most prolific hosts in the discovery of giant NCLDVs, for possible DNA inserts of viral origin...
November 3, 2016: Genome Biology and Evolution
Brice A J Sarver, John R Demboski, Jeffrey M Good, Nicholas Forshee, Samuel S Hunter, Jack Sullivan
Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression...
October 26, 2016: Genome Biology and Evolution
Lucie Mota, Rubén Torices, João Loureiro
Chromosome number changes during the evolution of angiosperms are likely to have played a major role in speciation. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. Specifically, a phylogenetic supertree of this family was used to reconstruct the ancestral chromosome number and infer genomic events...
October 26, 2016: Genome Biology and Evolution
Phuong Cao Thi Ngoc, Robert Greenhalgh, Wannes Dermauw, Stephane Rombauts, Sabina Bajda, Vladimir Zhurov, Miodrag Grbić, Yves Van de Peer, Thomas Van Leeuwen, Pierre Rouzé, Richard M Clark
While mechanisms to detoxify plant produced, anti-herbivore compounds have been associated with plant host use by herbivores, less is known about the role of chemosensory perception in their life histories. This is especially true for generalists, including chelicerate herbivores that evolved herbivory independently from the more studied insect lineages. To shed light on chemosensory perception in a generalist herbivore, we characterized the chemosensory receptors (CRs) of the chelicerate two-spotted spider mite, Tetranychus urticae, an extreme generalist...
October 26, 2016: Genome Biology and Evolution
M D Ramirez, A N Pairett, M S Pankey, J M Serb, D I Speiser, A J Swafford, T H Oakley
The opsin gene family encodes key proteins animals use to sense light and has expanded dramatically since it originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals...
October 26, 2016: Genome Biology and Evolution
Shoukai Yu, Bernardo Lemos
Ribosomal rRNAs account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, while the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs)...
October 25, 2016: Genome Biology and Evolution
Lingyang Xu, Ryan J Haasl, Jiajie Sun, Yang Zhou, Derek M Bickhart, Junya Li, Jiuzhou Song, Tad S Sonstegard, Curtis P Van Tassell, Harris A Lewin, George E Liu
Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2-6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs...
October 24, 2016: Genome Biology and Evolution
Ming Wen, Munan Xie, Lian He, Yushuai Wang, Suhua Shi, Tian Tang
Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11...
October 24, 2016: Genome Biology and Evolution
Dhriti Sengupta, Ananyo Choudhury, Analabha Basu, Michèle Ramsay
Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto-Burman (ATB) and Ancestral Austro-Asiatic (AAA)...
October 23, 2016: Genome Biology and Evolution
Cécile Monat, Bérengère Pera, Marie-Noelle Ndjiondjop, Mounirou Sow, Christine Tranchant-Dubreuil, Leila Bastianelli, Alain Ghesquière, Francois Sabot
Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared to its Asian cousin O. sativa A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo 3 different cultivars from O. glaberrima After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals...
October 20, 2016: Genome Biology and Evolution
Monica H Solbakken, Matthew L Rise, Kjetill S Jakobsen, Sissel Jentoft
Great genetic variability among teleost immunomes, with gene losses and expansions of central adaptive and innate components, has been discovered through genome sequencing over the last few years. Here, we demonstrate that the innate Myxovirus resistance gene (Mx) is lost from the ancestor of Gadiformes and the closely related Stylephorus chordatus, thus predating the loss of Major Histocompatibility Complex class II (MHCII) in Gadiformes. Although the functional implication of Mx loss is still unknown, we demonstrate that this loss is one of several ancient events appearing in successive order throughout the evolution of teleost immunity...
October 19, 2016: Genome Biology and Evolution
Stéphane Boissinot, Akash Sookdeo
The abundance and diversity of the LINE-1 (L1) retrotransposon differ greatly among vertebrates. Mammalian genomes contain hundred of thousands L1s that have accumulated since the origin of mammals. A single group of very similar elements is active at a time in mammals, thus a single lineage of active families has evolved in this group. In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies...
October 19, 2016: Genome Biology and Evolution
Jordon Rahaman, Jessica Siltberg-Liberles
Within the last 15 years, two related coronaviruses (SARS-CoV and MERS-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared to many other virus families. Since intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context...
October 19, 2016: Genome Biology and Evolution
Liandong Yang, Zhaolei Zhang, Shunping He
Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level...
October 13, 2016: Genome Biology and Evolution
Pooja Narang, Melissa A Wilson Sayres
Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes...
October 4, 2016: Genome Biology and Evolution
A Fijarczyk, K Dudek, W Babik
Host-pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases...
October 4, 2016: Genome Biology and Evolution
Atma M Ivancevic, R Daniel Kortschak, Terry Bertozzi, David L Adelson
LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to 'jump' around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterised domain organisation. For the past 30 years, model organisms have been used to define L1s as 6-8kb sequences containing a 5'-UTR, two open reading frames working harmoniously in cis, and a 3'-UTR with a polyA tail...
October 3, 2016: Genome Biology and Evolution
Mihai Miclaus, Ovidiu Balacescu, Ioan Has, Loredana Balacescu, Voichita Has, Dana Suteu, Samuel Neuenschwander, Irene Keller, Rémy Bruggmann
The genomes of the two plant organelles encode for a relatively small number of proteins. Thus, nuclear genes encode the vast majority of their proteome. Organelleto-nucleus communication takes place through retrograde signaling (RS) pathways. Signals relayed through RS pathways have an impact on nuclear gene expression (NGE) but their target-genes remain elusive in a normal state of the cell (considering that only mutants and stress have been used so far). Here we use maize cytolines as an alternative. The nucleus of a donor line was transferred into two other cytoplasmic environments through at least nine back-crosses, in a time-span of more than 10 years...
October 3, 2016: Genome Biology and Evolution
Kirill V Mikhailov, Timur G Simdyanov, Vladimir V Aleoshin
Metchnikovellidae are a group of unusual microsporidians that lack some of the defining ultrastructural features characteristic of derived Microsporidia and are thought to be one of their earliest-branching lineages. The basal position of metchnikovellids was never confirmed by molecular phylogeny in published research, and thus far no genomic data for this group were available. In this work we obtain a partial genome of metchnikovellid Amphiamblys sp. using multiple displacement amplification, next-generation sequencing, and metagenomic binning approaches...
September 30, 2016: Genome Biology and Evolution
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