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Genome Biology and Evolution

Xuebin Qi, Qu Zhang, Yaoxi He, Lixin Yang, Xiaoming Zhang, Peng Shi, Linping Yang, Zhengheng Liu, Fuheng Zhang, Fengyun Liu, Shiming Liu, Tianyi Wu, Chaoying Cui, Ouzhuluobu, Caijuan Bai, Baimakangzhuo, Jianlin Han, Shengguo Zhao, Chunnian Liang, Bing Su
Yak is one of the largest native mammalian species at the Himalayas, the highest plateau area in the world with an average elevation of more than 4,000 meters above the sea level. Yak is well adapted to high altitude environment with a set of physiological features for a more efficient blood flow for oxygen delivery under hypobaric hypoxia. Yet, the genetic mechanism underlying its adaptation remains elusive. We conducted a cross-tissue, cross-altitude and cross-species study to characterize the transcriptomic landscape of domestic yaks...
December 4, 2018: Genome Biology and Evolution
Christopher Paight, Claudio H Slamovits, Mary Beth Saffo, Christopher E Lane
The Phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasitic sister taxon, Cardiosporidium, revealing an ancestral purine degradation pathway thought to have been lost early in apicomplexan evolution. The predicted localization of many of the purine degradation enzymes to peroxisomes, and the in silico identification of a full set of peroxisome proteins, indicates that loss of both features in other apicomplexans occurred multiple times...
November 30, 2018: Genome Biology and Evolution
R J Nuckels, C C Nice, D M García
We analyzed evolutionary rates of conserved, duplicated myosin V (myo5) genes in nine teleost species to examine the outcomes of duplication events. Syntenic analysis and ancestral chromosome mapping suggest one tandem gene duplication event leading to the appearance of myo5a and myo5c, two rounds of whole genome duplication for vertebrates, and an additional round of whole genome duplication for teleosts account for the presence and location of the myo5 genes and their duplicates in teleosts and other vertebrates and the timing of the duplication events...
November 29, 2018: Genome Biology and Evolution
T A Whelan, N T Lee, R C H Lee, N M Fast
Spliceosomal introns are ubiquitous features of eukaryotic genomes, but the mechanisms responsible for their loss and gain are difficult to identify. Microsporidia are obligate intracellular parasites that have significantly reduced genomes and, as a result, have lost many if not all of their introns. In the microsporidian Encephalitozoon cuniculi, a relatively long intron was identified and was spliced at higher levels than the remaining introns. This long intron is part of a set of unique introns in two unrelated genes that show high levels of sequence conservation across diverse microsporidia...
November 29, 2018: Genome Biology and Evolution
Qiulan Luo, Bian Chao, Ming Tao, Yu Huang, Yihong Zheng, Yunyun Lv, Li Jia, Chaogang Wang, Xinxin You, Bin Jia, Junmin Xu, Jiancheng Li, Ze Li, Qiong Shi, Zhangli Hu
Haematococcus pluvialis is a freshwater species of Chlorophyta, family Haematococcaceae. It is well known for its capacity to synthesize high amounts of astaxanthin, which is a strong antioxidant that has been utilized in aquaculture and cosmetics. To improve astaxanthin yield and to establish genetic resources for H. pluvialis, we performed whole-genome sequencing, assembly, and annotation of this green microalga. A total of 83.1 Gigabases (Gb) of raw reads were sequenced. After filtering the raw reads, we subsequently generated a draft assembly with a genome size of 669...
November 29, 2018: Genome Biology and Evolution
Camille Berthelot, Jane Clarke, Thomas Desvignes, H William Detrich, Paul Flicek, Lloyd S Peck, Michael Peters, John H Postlethwait, Melody S Clark
The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whilst successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding and degrading proteins at their ambient temperatures of -1.86 °C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold...
November 29, 2018: Genome Biology and Evolution
Evandro Ferrada
The propensity of protein sites to be occupied by any of the 20 amino acids is known as site-specific amino acid preferences (SSAP). Under the assumption that SSAP are conserved among homologs, they can be used to parameterize evolutionary models for the reconstruction of accurate phylogenetic trees. However, simulations and experimental studies have not been able to fully assess the relative conservation of SSAP as a function of sequence divergence between protein homologs. Here we implement a computational procedure to predict the SSAP of proteins based on the effect of changes in thermodynamic stability upon mutation...
November 29, 2018: Genome Biology and Evolution
Luca Freschi, Antony T Vincent, Julie Jeukens, Jean-Guillaume Emond-Rheault, Irena Kukavica-Ibrulj, Marie-Josée Dupont, Steve J Charette, Brian Boyle, Roger C Levesque
The huge increase in the availability of bacterial genomes led us to a point in which we can investigate and query pan-genomes, i.e. the full set of genes of a given bacterial species or clade. Here, we used a dataset of 1,311 high-quality genomes from the human pathogen Pseudomonas aeruginosa, 619 of which were newly sequenced, to show that a pan-genomic approach can greatly refine the population structure of bacterial species, provide new insights to define species boundaries, and generate hypotheses on the evolution of pathogenicity...
November 29, 2018: Genome Biology and Evolution
Vaishali Katju, Ulfar Bergthorsson
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurement of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations...
November 26, 2018: Genome Biology and Evolution
Corrinne E Grover, Mark A Arick Ii, Adam Thrash, Justin L Conover, William S Sanders, Daniel G Peterson, James E Frelichowski, Jodi A Scheffler, Brian E Scheffler, Jonathan F Wendel
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33X genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following trans-oceanic dispersal from Africa about 6.6 mya, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0...
November 23, 2018: Genome Biology and Evolution
Diego Alonso, Maria Vittoria Mancini, Claudia Damiani, Alessia Cappelli, Irene Ricci, Marcus Vinicius Niz Alvarez, Claudio Bandi, Paulo Ribolla, Guido Favia
Symbiosis is now recognized as a driving force in evolution, a role that finds its ultimate expression in the variety of associations bonding insects with microbial symbionts. These associations have contributed to the evolutionary success of insects, with the hosts acquiring the capacity to exploit novel ecological niches, and the symbionts passing from facultative associations to obligate, mutualistic symbioses. In bacterial symbiont of insects, the transition from the free-living life style to mutualistic symbiosis often resulted in a reduction in the genome size, with the generation of the smallest bacterial genomes thus far described...
November 23, 2018: Genome Biology and Evolution
Maximiliane Sparwel, Liliya Doronina, Gennady Churakov, Anja Stegemann, Jürgen Brosius, Terence J Robinson, Jürgen Schmitz
The order Lagomorpha unifies pikas (Ochotonidae) and the hares plus rabbits (Leporidae). Phylogenetic reconstructions of the species within the family Leporidae based on traditional morphological or molecular sequence data provide support for conflicting hypotheses. The retroposon presence/absence patterns analyzed in this study revealed strong support for the broadly accepted splitting of lagomorphs into ochotonids and leporids with Pronolagus as the first divergence in the leporid tree. Furthermore, the retroposon presence/absence patterns nested the rare volcano rabbit, Romerolagus diazi, within an unresolved network of deeper leporid relationships and provide the first homoplasy-free image of incomplete lineage sorting and/or ancestral hybridization/introgression in rapidly radiated Leporidae...
November 23, 2018: Genome Biology and Evolution
Piotr Minias, Ewa Pikus, Linda A Whittingham, Peter O Dunn
The evolution of the Major Histocompatibility Complex (MHC) is shaped by frequent gene duplications and deletions, which generate extensive variation in the number of loci (gene copies) between different taxa. Here, we collected estimates of copy number at the MHC for over 250 bird species from 68 families. We found contrasting patterns of copy number evolution between MHC class I and class IIB, which encode receptors for intra- and extra-cellular pathogens, respectively. Across the avian evolutionary tree, there was evidence of accelerated evolution and stabilizing selection acting on copy number at class I, while copy number at class IIB was primarily influenced by fluctuating selection and drift...
November 23, 2018: Genome Biology and Evolution
Yuanning Li, Kevin M Kocot, Michael G Tassia, Johanna T Cannon, Matthias Bernt, Kenneth M Halanych
The diverse array of codon reassignments has demonstrated that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced hindering our understanding of mitochondrial genome evolution within Deuterostomia...
November 23, 2018: Genome Biology and Evolution
Ling-Yi Jia, Li Chen, Laurent Keller, John Wang, Jin-Hua Xiao, Da-Wei Huang
The Dmrt (Doublesex and Mab-3 Related Transcription factor) genes are transcription factors crucial for sex determination and sexual differentiation. In some social insects, Doublesex (dsx) exhibits widespread caste-specific expression across different tissues and developmental stages and has been suggested as a candidate gene for regulating division of labor in social insects. We therefore conducted a molecular evolution analysis of the Dmrt gene family in 20 ants. We found that the insect-specific oligomerization domain of DSX, oligomerization domain 2 (OD2), was absent in all ants, except for the two phylogenetically basal ant species (Ponerinae), whose social structure and organization resemble the presumed ancestral condition in ants...
November 22, 2018: Genome Biology and Evolution
Tomoyuki Kado, Hideki Innan
We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, while the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampyrum roseum) are facultative parasites. By using reference genome sequences and/or transcriptomes of 14 species from Fabaceae and Poaceae, their major host families, we detected 106 horizontally transferred genes (HGT genes), only in the genomes of the two obligate parasites (22 and 84 for O...
November 8, 2018: Genome Biology and Evolution
Mariana Aline Silva Artur, Tao Zhao, Wilco Ligterink, M Eric Schranz, Henk W M Hilhorst
Late Embryogenesis Abundant (LEA) proteins include eight multi-gene families that are expressed in response to water loss during seed maturation and in vegetative tissues of desiccation tolerant species. To elucidate LEA proteins evolution and diversification, we performed a comprehensive synteny and phylogenetic analyses of the eight gene families across 60 complete plant genomes. Our integrated comparative genomic approach revealed that synteny conservation and diversification contributed to LEA family expansion and functional diversification in plants...
November 8, 2018: Genome Biology and Evolution
Mindia Haryono, Yi-Ming Tsai, Chien-Tin Lin, Fan-Chen Huang, Yan-Chen Ye, Wen-Ling Deng, Hau-Hsuan Hwang, Chih-Horng Kuo
The genus Agrobacterium contains a group of plant-pathogenic bacteria that have been developed into an important tool for genetic transformation of eukaryotes. To further improve this biotechnology application, a better understanding of the natural genetic variation is critical. During the process of isolation and characterization of wild-type strains, we found a novel strain (i.e., NCHU2750) that resembles Agrobacterium phenotypically but exhibits high sequence divergence in several marker genes. For more comprehensive characterization of this strain, we determined its complete genome sequence for comparative analysis and performed pathogenicity assays on plants...
November 6, 2018: Genome Biology and Evolution
Raquel Assis
Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here, I address this question on a genome-wide scale by applying a novel branch-based statistic of lineage-specific expression divergence, LED, to RNA-seq data from nine tissues of the wild grass Brachypodium distachyon and its domesticated relatives Oryza sativa japonica (rice) and Sorghum bicolor (sorghum)...
November 6, 2018: Genome Biology and Evolution
Baojun Wu, Zhangyi Xu, Alicia Knudson, Alexis Carlson, Naiyao Chen, Sam Kovaka, Kurt LaButti, Anna Lipzen, Christa Pennachio, Robert Riley, Wendy Schakwitz, Kiwamu Umezawa, Robin A Ohm, Igor V Grigoriev, László G Nagy, John Gibbons, David Hibbett
Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15581-15380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA)...
November 6, 2018: Genome Biology and Evolution
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