Abstract：
:Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a large number of genomes is of key importance in understanding the impact of HGT in the evolution of prokaryotes. We developed a method for the detection of genes that potentially originated by HGT based on the comparison of BLAST scores between homologous genes to 16S rRNA-based phylogenetic distances between the involved organisms. The approach was applied to 697 prokaryote genomes and estimated that in average approximately 15% of the genes in prokaryote genomes originated by HGT, with a clear correlation between the proportion of predicted HGT genes and the size of the genome. The methodology was strongly supported by evolutionary relationships, as tested by the direct phylogenetic reconstruction of many of the HGT candidates. Studies performed with Escherichia coli W3110 genome clearly show that HGT proteins have fewer interactions when compared to those predicted as vertical inherited, an indication that the number of protein partners imposes limitations to horizontal transfer. A detailed functional classification confirms that genes related to protein translation are vertically inherited, whereas interestingly, transport and binding proteins are strongly enriched among HGT genes. Because these genes are related to the cell exchange with their environment, their transfer most likely contributed to successful adaptation throughout evolution.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Paquola ACM,Asif H,Pereira CAB,Feltes BC,Bonatto D,Lima WC,Menck CFMdoi
10.1007/s00239-018-9836-xsubject
Has Abstractpub_date
2018-04-01 00:00:00pages
190-203issue
3-4eissn
0022-2844issn
1432-1432pii
10.1007/s00239-018-9836-xjournal_volume
86pub_type
杂志文章abstract：:We provide here evidence for a conserved regulatory element for transcription of the β-family globin genes based on a comparative study of 32 genes from 16 mammals. The element is characterized by the appearance of AA or TT dinucleotides in the A + T-rich region located 200-400 bp upstream of the cap sites. G-tracts 3...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9459-y
更新日期：2011-10-01 00:00:00
abstract：:Nuclear DNA contents were estimated by microdensitometry in five species of Akodon rodents: Arodon molinae, A. dolores, A. mollis, A. azarae, Bolomys obscurus) and in three chromosomal varieties of A. molinae (2n = 42; 2n = 43, 2n = 22). The data obtained showed that the species with the highest DNA content was B. obs...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101640
更新日期：1983-01-01 00:00:00
abstract：:We studied the genomic organization of Hox genes in Atlantic salmon (Salmo salar) and made comparisons to that in rainbow trout (Oncorhynchus mykiss), another member of the family Salmonidae. We used these two species to test the hypothesis that the Hox genes would provide evidence for a fourth round of duplication (4...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0338-7
更新日期：2005-11-01 00:00:00
abstract：:Type 1 (archaeal) rhodopsins and related rhodopsin-like proteins had been described in a few halophile archaea, gamma-proteobacteria, a single cyanobacteria, some fungi, and a green alga. In exhaustive database searches, we detected rhodopsin-related sequences derived not only from additional fungal species but also f...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2557-8
更新日期：2004-03-01 00:00:00
abstract：:Mutational bias toward expansion or contraction of simple sequence repeats (SSRs) is referred to as directionality of SSR evolution. In this communication, we report the mutational bias exhibited by mononucleotide SSRs occurring in the non-coding regions of several prokaryotic genomes. Our investigations revealed that...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-012-9491-6
更新日期：2012-04-01 00:00:00
abstract：:We analyzed precursor messenger RNAs (pre-mRNAs) of 12 eukaryotic species. In each species, three groups of highly expressed genes, ribosomal proteins, heat shock proteins, and amino-acyl tRNA synthetases, were compared with a control group (randomly selected genes). The purine-pyrimidine (R-Y) composition of pre-mRNA...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0135-6
更新日期：2007-02-01 00:00:00
abstract：:The present work deals with the processes involved in the abiogenic polycondensation of nucleotides adsorbed on the clay mineral kaolinite under the action of ultraviolet (UV) radiation. The dependence of the yield of synthesis products on irradiation dose was studied. The maximum yield corresponds to a 6-h exposure. ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02100636
更新日期：1986-01-01 00:00:00
abstract：:The entire mitochondrial DNA control region (mtDNA D-loop) was sequenced in the seven extant species of Alectoris partridges. The D-loop length is very conserved (1155 +/- 2 nucleotides), and substitution rates are lower than for the mitochondrial cytochrome b gene of the same species, on average. Comparative analyses...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006402
更新日期：1998-10-01 00:00:00
abstract：:The trnT-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL intron, a group I intron, and the trnT-trnL and trnL-trnF intergenic spacers. We analyzed the evolution of the region in the three genera of the gymnosperm lineage Gnetales (Gnetum, Welwitschia, and Ephed...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0240-3
更新日期：2005-10-01 00:00:00
abstract：:To get deeper insight into the evolution of phosphoenolpyruvate carboxylase we have identified PEPC fragments (about 1,100 bp) of another 12 plants species not yet investigated in this context. The selected plants include one Chlorophyta, two Bryophyta, four Pteridophyta, and five Spermatophyta species. The obtained p...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006277
更新日期：1998-01-01 00:00:00
abstract：:The level reached by the optimization of the polarity distances during the evolution of the genetic code was investigated. The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary min...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02103616
更新日期：1989-10-01 00:00:00
abstract：:In studies of molecular evolution, the assumption that protein evolution is reversible has often been made, but rarely tested. Here we use a large set of orthologous murid protein coding sequences to perform a simple test of reversibility, and find no evidence to reject the assumption of reversibility in protein evolu...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010176
更新日期：2001-05-01 00:00:00
abstract：:The nearly neutral theory attributes most nucleotide substitution and polymorphism to genetic drift acting on weakly selected mutants, and assumes that the selection coefficients for these mutants are drawn from a continuous distribution. This means that parameter estimation can require numerical integration, and this...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9146-9
更新日期：2008-10-01 00:00:00
abstract：:Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual, highly conserved, elements of the B1 SINE family were identified from t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010087
更新日期：2000-09-01 00:00:00
abstract：:The glycosylation characteristics of the digestive enzyme ribonuclease are summarized. The evolutionary role of this posttranslational modification is discussed and evidence is presented that selection has much influence on the presence or absence of carbohydrate in glycoproteins and on the positions of the carbohydra...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099959
更新日期：1986-01-01 00:00:00
abstract：:In mammals, chicken-type (c-type) lysozymes are part of the innate immune system, killing bacteria by degrading peptidoglycan in their cell walls. Many of the studies on the evolution of c-type lysozymes have focused on its new digestive function, including the duplicated stomach lysozymes in ruminants. Similarly, in ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-019-09910-7
更新日期：2019-12-01 00:00:00
abstract：:Two catalytic functions were required, minimally, for the appearance of DNA in evolution: a ribonucleotide reductase (RNR) and a reverse transcriptase (RT). If one accepts the explanatory strength of the RNA world model, it is clear that DNA molecules arose in the RNA world at some stage during the early evolution of ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006368
更新日期：1998-08-01 00:00:00
abstract：:By a chromosome walking strategy the DNA region from Methanococcus vannielii flanking the genes for protein synthesis elongation factor (EF) 1 alpha and EF-2 was cloned and sequenced. A gene organization of 5' - beta' - open reading frame (ORF) 1 - ORF2 - S12 - S7 - EF-2 - EF-1 alpha - S10 - ORF3 - ORF4 - 3' was found...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02106178
更新日期：1989-07-01 00:00:00
abstract：:Sequences were obtained from five species of rodents that are orthologous to an H2a histone pseudogene from Mus musculus. The pseudogene is part of the cluster of replication-dependent histone genes found on Mus musculus chromosome 13. Comparative analysis of these five sequences together with the previously published...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006312
更新日期：1998-03-01 00:00:00
abstract：:Available molecular and biochemical data offer conflicting evidence for the origin of the cyanelle of Cyanophora paradoxa. We show that the similarity of cyanelle and green chloroplast sequences is probably a result of these two lineages independently developing the same pattern of directional nucleotide change (subst...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00182392
更新日期：1992-02-01 00:00:00
abstract：:The observed and expected frequencies of occurrence of microsatellites in the yeast Saccharomyces cerevisiae were investigated. In all cases, the observed frequencies exceeded the expected ones. In contrast to predictions by Messier et al. (1996), there is no critical number of repeats beyond which the observed freque...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006474
更新日期：1999-03-01 00:00:00
abstract：:The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9068-6
更新日期：2008-03-01 00:00:00
abstract：:Universal scale of the sequence conservation has been recently introduced based on omnipresence of the protein sequence motifs across species. A large spectrum of short sequences, up to eight residues has been found to reside in all or almost all prokaryotic organisms. By this discovery a principally novel quantitativ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0190-4
更新日期：2006-11-01 00:00:00
abstract：:With the aim of elucidating the evolutionary processes of the kringle and protease domains in serine proteases which are involved with the system of blood coagulation and fibrinolysis, we constructed phylogenetic trees for the kringle and protease domains, separately, by use of amino acid sequence data. The phylogenet...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00163238
更新日期：1995-03-01 00:00:00
abstract：:Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color d...
journal_title：Journal of molecular evolution
pub_type： 杂志文章,评审
doi：10.1007/s00239-019-09902-7
更新日期：2020-01-01 00:00:00
abstract：:Computer analyses of various genome sequences revealed the existence of certain periodical patterns of adenine-adenine dinucleotides (ApA). For each genome sequence of 13 eubacteria, 3 archaebacteria, 10 eukaryotes, 60 mitochondria, and 9 chloroplasts, we counted frequencies of ApA dinucleotides at each downstream pos...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006541
更新日期：1999-08-01 00:00:00
abstract：:The recent availability of genome sequences of four different Fusarium species offers the opportunity to perform extensive comparative analyses, in particular of repeated sequences. In a recent work, the overall content of such sequences in the genomes of three phylogenetically related Fusarium species, F. graminearum...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9472-1
更新日期：2011-10-01 00:00:00
abstract：:Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9348-9
更新日期：2010-05-01 00:00:00
abstract：:The possibility of surface catalysed condensation of unsubstituted amino acids on kaolinite in aqueous systems at elevated temperatures was investigated; no evidence of clay catalysed polycondensation has been found. The thermodynamic feasibility of the hypothetical lysine/dilysine condensation reaction in the tempera...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01733261
更新日期：1978-12-29 00:00:00
abstract：:This paper presents an essentially new method used to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential p...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160324
更新日期：1995-10-01 00:00:00
