Abstract:
:The spacer between the 16S and 23S rRNA genes of the chloroplast DNA has been implicated as an origin of replication in several species of plants. In the evening primrose, Oenothera, this site was found to vary greatly in size, with plastid genomes (plastomes) being readily distinguished. To determine whether plastome "strength" in transmission could be correlated with variation at oriB, the 16S rRNA-trnI spacer was sequenced from five plastomes. The size variation was found to be due to differential amplification (and deletion) of combinations of sequences belonging to seven families of direct repeats. From these comparisons, one short series of direct repeats and one region capable of forming a hairpin structure were identified as candidates for the factor that could be responsible for the differences between strong and weak plastome types. Ample sequence variation allowed phylogenetic inferences to be made about the relationships among the plastomes. Phylogenetic trees also could be constructed for most of the families of direct repeats. The amplifications and deletions of repeats that account for the size variation at oriB are proposed to have occurred through extensive replication slippage at this site.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Sears BB,Stoike LL,Chiu WLdoi
10.1093/oxfordjournals.molbev.a025645subject
Has Abstractpub_date
1996-07-01 00:00:00pages
850-63issue
6eissn
0737-4038issn
1537-1719journal_volume
13pub_type
杂志文章abstract::This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the ori...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040081
更新日期:1993-11-01 00:00:00
abstract::How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa288
更新日期:2020-11-10 00:00:00
abstract::Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental ad...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw249
更新日期:2017-03-01 00:00:00
abstract::A detailed assessment of the evolution and phylogenetic utility of two genes, ftsZ and wsp, was used to investigate the origin of male-killing Wolbachia, previously isolated from the ladybird Adalia bipunctata and the butterfly Acraea encedon. The analysis included almost all available sequences of B-group Wolbachia a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026338
更新日期:2000-04-01 00:00:00
abstract::Gene unscrambling in spirotrichous ciliates involves massive genome-wide DNA deletion and rearrangement events during development. During each sexual cycle, the somatic nucleus (macronucleus) regenerates from the germ line nucleus (micronucleus). Development of the polyploid somatic genome requires programmed DNA dele...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj089
更新日期:2006-04-01 00:00:00
abstract::The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy237
更新日期:2019-05-01 00:00:00
abstract::Positive Darwinian selection promotes fixations of advantageous mutations during gene evolution and is probably responsible for most adaptations. Detecting positive selection at the DNA sequence level is of substantial interest because such information provides significant insights into possible functional alterations...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh117
更新日期:2004-07-01 00:00:00
abstract::Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a G...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss265
更新日期:2013-03-01 00:00:00
abstract::Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERN...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa038
更新日期:2020-06-01 00:00:00
abstract::Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process, we examined the fate of the 10-member-large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. ...
journal_title:Molecular biology and evolution
pub_type: 历史文章,杂志文章
doi:10.1093/molbev/msi170
更新日期:2005-09-01 00:00:00
abstract::Disturbances in the schedules of gene expression in developing interspecific fish hybrids have been used to draw inferences about the extent of gene regulatory divergence between species and about the degree to which this gene regulatory divergence is correlated with structural gene divergence, as estimated by genetic...
journal_title:Molecular biology and evolution
pub_type: 杂志文章,评审
doi:10.1093/oxfordjournals.molbev.a040349
更新日期:1985-05-01 00:00:00
abstract::Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr076
更新日期:2011-09-01 00:00:00
abstract::Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa221
更新日期:2021-01-23 00:00:00
abstract::A combination of three independent biological features, genomic organization, diagnostic amino acid sites, and rare indels, was used to elucidate the phylogeny of the vertebrate serpin (serine protease inhibitor) superfamily. A strong correlation between serpin gene families displaying (1) a conserved exon-intron patt...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003838
更新日期:2001-04-01 00:00:00
abstract::High-affinity antibodies arise within weeks of infection from the evolution of B-cell receptors under selection to improve antigen recognition. This rapid adaptation is enabled by the distribution of highly mutable "hotspot" motifs in B-cell receptor genes. High mutability in antigen-binding regions (complementarity d...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy024
更新日期:2018-05-01 00:00:00
abstract::During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj036
更新日期:2006-02-01 00:00:00
abstract::This study describes the origin and structural features of a mammalian gene, CGIN1 (Cousin of GIN1). CGIN1 proteins contain an NYN domain, retroviral RNase H and integrase domains, and a domain of unknown function (CGIN1 domain) that is also present in two other genes (N4BP1 and KIAA0323). We suggest that CGIN1 derive...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msp127
更新日期:2009-10-01 00:00:00
abstract::Genetic incompatibilities are commonly observed between hybridizing species. Although this type of isolating mechanism has received considerable attention, we have few examples describing how genetic incompatibilities evolve. We investigated the evolution of two loci involved in a classic example of a Bateson-Dobzhans...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst127
更新日期:2013-10-01 00:00:00
abstract::Members of the grass family (Poaceae) exhibit a broad range of inflorescence structures and other morphologies, making the grasses an interesting model system for studying the evolution of development. Here we present an analysis of the molecular evolution of FLORICAULA/LEAFY-like genes, which are important developmen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi095
更新日期:2005-04-01 00:00:00
abstract::The ribosome is responsible for protein synthesis in all living organisms. It is best known to exist around 3.5-3.7 Ga whereat life on Earth inhabited anoxic environment with abundant soluble irons. The RNAs and proteins are the two biopolymers that constitute the ribosome. However, both proteins and RNAs require meta...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz034
更新日期:2019-05-01 00:00:00
abstract::Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication ev...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx234
更新日期:2017-12-01 00:00:00
abstract::The cellobiose catabolic system of Escherichia coli K12 is being used to study the role of cryptic genes in evolution of new functions. Escherichia coli does not use beta-glucoside sugars; however, mutations in several loci can activate the cryptic bgl operon and permit growth on the beta-glucoside sugars arbutin and ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040310
更新日期:1984-02-01 00:00:00
abstract::Since the discovery of ING1 class II tumor suppressors in 1996, five different ING genes (ING1 to ING5) encoding proteins with highly conserved plant homeodomain (PHD) motifs and several splicing isoforms of the ING1 and ING2 gene have been identified. The ING family functions in DNA repair and apoptosis in response t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh256
更新日期:2005-01-01 00:00:00
abstract::We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that ar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025817
更新日期:1997-07-01 00:00:00
abstract::Cytochrome c oxidase (COX) consists of 13 subunits, 3 encoded in the mitochondrial genome and 10 in the nucleus. Little is known of the role of the nuclear-encoded subunits, some of which exhibit tissue-specific isoforms. Subunit VIa is unique in having tissue-specific isoforms in all mammalian species examined. We ex...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025798
更新日期:1997-06-01 00:00:00
abstract::Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv206
更新日期:2016-01-01 00:00:00
abstract::One of the most fundamental questions for understanding the origin of species is why genes that function to cause fertility in a pure-species genetic background fail to produce fertility in a hybrid genetic background. A related question is why the sex that is most often sterile or inviable in hybrids is the heterogam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg119
更新日期:2003-07-01 00:00:00
abstract::Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026215
更新日期:1999-09-01 00:00:00
abstract::Partial 18S rRNA sequence of the nemertine Cerebratulus lacteus was obtained and compared with those of coelomate metazoans and acoelomate platyhelminths to test whether nemertines share a most recent common ancestor with the platyhelminths, as traditionally has been implied, or whether nemertines lie within a protost...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040716
更新日期:1992-03-01 00:00:00
abstract::Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsist...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn176
更新日期:2008-11-01 00:00:00