Abstract:
:MicroRNAs (miRNAs) are short endogenous RNA molecules that regulate gene expression at the posttranscriptional level and have been shown to play critical roles during animal development. The identification and comparison of miRNAs in metazoan species are therefore paramount for our understanding of the evolution of body plans. We have characterized 203 miRNAs from the red flour beetle Tribolium castaneum by deep sequencing of small RNA libraries. We can conclude, from a single study, that the Tribolium miRNA set is at least 15% larger than that in the model insect Drosophila melanogaster (despite tens of high-throughput sequencing experiments in the latter). The rate of birth and death of miRNAs is high in insects. Only one-third of the Tribolium miRNA sequences are conserved in D. melanogaster, and at least 18 Tribolium miRNAs are conserved in vertebrates but lost in Drosophila. More than one-fifth of miRNAs that are conserved between Tribolium and Drosophila exhibit changes in the transcription, genomic organization, and processing patterns that lead to predicted functional shifts. For example, 13% of conserved miRNAs exhibit seed shifting, and we describe arm-switching events in 11% of orthologous pairs. These shifts fundamentally change the predicted targets and therefore function of orthologous miRNAs. In general, Tribolium miRNAs are more representative of the insect ancestor than Drosophila miRNAs and are more conserved in vertebrates.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Marco A,Hui JH,Ronshaugen M,Griffiths-Jones Sdoi
10.1093/gbe/evq053subject
Has Abstractpub_date
2010-01-01 00:00:00pages
686-96issn
1759-6653pii
evq053journal_volume
2pub_type
杂志文章abstract::In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database we...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz208
更新日期:2019-10-01 00:00:00
abstract::Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic a...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt061
更新日期:2013-01-01 00:00:00
abstract::Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired sh...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu046
更新日期:2014-03-01 00:00:00
abstract::Conservation of function can be accompanied by obvious similarity of homologous sequences which may persist for billions of years (Iyer LM, Leipe DD, Koonin EV, Aravind L. 2004. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 146:11-31.). However, presumably homologous segments of ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt023
更新日期:2013-01-01 00:00:00
abstract::RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz232
更新日期:2019-11-01 00:00:00
abstract::The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity f...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv219
更新日期:2015-11-11 00:00:00
abstract::Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, howe...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa098
更新日期:2020-07-01 00:00:00
abstract::Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of geni...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt122
更新日期:2013-01-01 00:00:00
abstract::The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary pr...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy198
更新日期:2018-11-01 00:00:00
abstract::Many viroids and RNA viruses have genomes that exhibit secondary structure, with paired nucleotides forming stems and loops. Such structures violate a key assumption of most methods of phylogenetic reconstruction, that sequence change is independent among sites. However, phylogenetic analyses of these transmissible ag...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx273
更新日期:2018-02-01 00:00:00
abstract::Hemerythrins and hemocyanins are respiratory proteins present in some of the most ecologically diverse animal lineages; however, the precise evolutionary history of their enzymatic domains (hemerythrin, hemocyanin M, and tyrosinase) is still not well understood. We survey a wide dataset of prokaryote and eukaryote gen...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt102
更新日期:2013-01-01 00:00:00
abstract::Bitter taste perception likely evolved as a protective mechanism against the ingestion of harmful compounds in food. The evolution of the taste receptor type 2 (TAS2R) gene family, which encodes the chemoreceptors that are directly responsible for the detection of bitter compounds, has therefore been of considerable i...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq027
更新日期:2010-07-12 00:00:00
abstract::Recent whole-genome approaches to microbial phylogeny have emphasized partitioning genes into functional classes, often focusing on differences between a stable core of genes and a variable shell. To rigorously address the effects of partitioning and combining genes in genome-level analyses, we developed a novel techn...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr121
更新日期:2012-01-01 00:00:00
abstract::Coliphage phi1, which was isolated for phage therapy in the Republic of Georgia, is closely related to the T-like myovirus RB49. The approximately 275 open reading frames encoded by each phage have an average level of amino acid identity of 95.8%. RB49 lacks 7 phi1 genes while 10 phi1 genes are missing from RB49. Most...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq006
更新日期:2010-02-01 00:00:00
abstract::The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatale...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv260
更新日期:2016-04-06 00:00:00
abstract::Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz053
更新日期:2019-04-01 00:00:00
abstract::Discoba (Excavata) is an evolutionarily important group of eukaryotes that includes Jakobida, with the most bacterial-like mitochondrial genomes known, and Euglenozoa, many of which have extensively fragmented mitochondrial genomes. However, little is known about the mitochondrial genomes of Heterolobosea, the third m...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx086
更新日期:2017-05-01 00:00:00
abstract::The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv244
更新日期:2015-12-08 00:00:00
abstract::The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr047
更新日期:2011-01-01 00:00:00
abstract::Theory suggests that biological modularity and robustness allow for maintenance of fitness under mutational change, and when this change is adaptive, for evolvability. Empirical demonstrations that these traits promote evolvability in nature remain scant however. This is in part because modularity, robustness, and evo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr046
更新日期:2011-01-01 00:00:00
abstract::Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model fo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz205
更新日期:2019-10-01 00:00:00
abstract::Intronic DNA is a major component of eukaryotic genes and genomes and can be subject to selective constraint and have functions in gene regulation. Intron size is of particular interest given that it is thought to be the target of a variety of evolutionary forces and has been suggested to be linked ultimately to vario...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs070
更新日期:2012-01-01 00:00:00
abstract::Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled th...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa108
更新日期:2020-07-01 00:00:00
abstract::Human-specific small insertions and deletions (HS indels, with lengths <100 bp) are reported to be ubiquitous in the human genome. However, whether these indels contribute to human-specific traits remains unclear. Here we employ a modified McDonald-Kreitman (MK) test and a combinatorial population genetics approach to...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evp041
更新日期:2009-10-20 00:00:00
abstract::Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment (LTEE) with Escherichia coli have also diversified extensively in nature. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx064
更新日期:2017-04-01 00:00:00
abstract::In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx155
更新日期:2017-09-01 00:00:00
abstract::Acetyl-CoA carboxylase (ACCase) is the key regulator of fatty acid biosynthesis. In most plants, ACCase exists in two locations (cytosol and plastids) and in two forms (homomeric and heteromeric). Heteromeric ACCase comprises four subunits, three of them (ACCA-C) are nuclear encoded (nr) and the fourth (ACCD) is usual...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz059
更新日期:2019-06-01 00:00:00
abstract::Vomeronasal sensitivity is important for detecting intraspecific pheromonal cues as well as environmental odorants and is involved in mating, social interaction, and other daily activities of many vertebrates. Two large families of seven-transmembrane G-protein-coupled receptors, V1rs and V2rs, bind to various ligands...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr039
更新日期:2011-01-01 00:00:00
abstract::Insertion sequences (ISs) are mobile genetic elements in bacterial genomes. In general, intergenic IS elements are probably less deleterious for their hosts than intragenic ISs, simply because they have a lower likelihood of disrupting native genes. However, since promoters, Shine-Dalgarno sequences, and transcription...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evq040
更新日期:2010-01-01 00:00:00
abstract::The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host im...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy124
更新日期:2018-09-01 00:00:00