Abstract：
:The genome organization of the Hardness locus in the tribe Triticeae constitutes an excellent model for studying the mechanisms of evolution that played a role in the preservation and potential functional innovations of duplicate genes. Here we applied the nonsynonymous-synonymous rate ratio (d ( N )/d ( S ) or omega) to measure the selective pressures at the paralogous puroindoline-a (Pina), puroindoline-b (Pinb), and grain softness protein-1 (Gsp-1) genes located at this locus. Puroindolines represent the molecular-genetic basis of grain texture. In addition, the puroindoline gene products have antimicrobial properties with potential role in plant defense. We document the complete coding sequences from the Triticum/Aegilops taxa, rye and barley including the A, D, C, H, M, N, R, S, and U genomes of the Triticeae. Maximum likelihood analyses performed on Bayesian phylogenetic trees showed distinct evolutionary patterns among Pina, Pinb, and Gsp-1. Positive diversifying selection appeared to drive the evolution of at least one of the three genes examined, suggesting that adaptive forces have operated at this locus. Results evidenced positive selection (omega > 4) at Pina and detected amino acid residues along the mature PIN-a protein with a high probability (>95%) of having evolved under adaptation. We hypothesized that positive selection at the Pina region is congruent with its role as a plant defense gene.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Massa AN,Morris CFdoi
10.1007/s00239-005-0292-zsubject
Has Abstractpub_date
2006-10-01 00:00:00pages
526-36issue
4eissn
0022-2844issn
1432-1432journal_volume
63pub_type
杂志文章abstract：:We obtained and studied HIV-1 sequences with a known sampling year from three outbreaks of the HIV-1 epidemic: 141 env V3 (270 nt) sampled between 1984 and 1992 and 117 pol prot/RT (804 nt) sequences sampled between 1986 and 1999 from Dutch homosexual men and injecting drug users (IDUs), as well as 77 env V3 sequences...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0070-5
更新日期：2002-05-01 00:00:00
abstract：:The evolutionary relationships of four eukaryotic kingdoms--Animalia, Plantae, Fungi, and Protista--remain unclear. In particular, statistical support for the closeness of animals to fungi rather than to plants is lacking, and a preferred branching order of these and other eukaryotic lineages is still controversial ev...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02198844
更新日期：1996-02-01 00:00:00
abstract：:DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once aligned with their Drosophila counterparts, sequence and base content comparisons were carried out. Sequence identity was found to be high overall, except for six regions that displ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173183
更新日期：1995-12-01 00:00:00
abstract：:Response regulators of bacterial sensory transduction systems generally consist of receiver module domains covalently linked to effector domains. The effector domains include DNA binding and/or catalytic units that are regulated by sensor kinase-catalyzed aspartyl phosphorylation within their receiver modules. Most re...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00167109
更新日期：1995-02-01 00:00:00
abstract：:Using gene genealogies constructed from gene sequence data, we show that both the mucosal and cutaneous papillomaviruses (PV)-supergroups A and B-appear to have been transmitted through susceptible populations faster than exponentially. The data and methods involved (1) examining the PV database for phylogenetic signa...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006136
更新日期：1997-02-01 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：:The monotremes, the duck-billed platypus and the echidnas, are characterized by a number of unique morphological characteristics, which have led to the common belief that they represent the living survivors of an ancestral stock of mammals. Analysis of new data from the complete mitochondrial (mt) genomes of a second ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0019-8
更新日期：2002-01-01 00:00:00
abstract：:Analysis of mitochondrial DNAs (mtDNAs) from parthenogenetic lizards of the Heteronotia binoei complex with restriction enzymes revealed an approximately 5-kb addition present in all 77 individuals. Cleavage site mapping suggested the presence of a direct tandem duplication spanning the 16S and 12S rRNA genes, the con...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02103135
更新日期：1991-11-01 00:00:00
abstract：:Hemoglobin Vancouver is a new abnormal hemoglobin with an amino acid substitution of the normal aspartyl residue 73 of the beta chain by a tyrosyl residue. It was discovered in a man of Chinese descent in association with beta thalassemia. It was subsequently detected in a sister in association with normal Hb A. The o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01796121
更新日期：1976-12-31 00:00:00
abstract：:Transfer RNA (tRNA) is the central intellectual property in the evolution of life on Earth. tRNA evolved from repeats and inverted repeats of known sequence. The anticodon and the T stem-loop-stems are homologs with significant conserved sequence identity. A number of models have been advanced to explain tRNA evolutio...
journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/s00239-020-09928-2
更新日期：2020-04-01 00:00:00
abstract：:The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Although their genomes differ substantially in size, these viruses share si...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2501-y
更新日期：2003-12-01 00:00:00
abstract：:In the maximum likelihood (ML) method for estimating a molecular phylogenetic tree, the pattern of nucleotide substitutions for computing likelihood values is assumed to be simpler than that of the actual evolutionary process, simply because the process, considered to be quite devious, is unknown. The problem, however...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099932
更新日期：1991-01-01 00:00:00
abstract：:Spermatogenesis is one of the most complex biological processes undergone by any organism, making it susceptible to perturbations that result in male sterility. Research has demonstrated that mutant phenotypes can be obtained from the disruption of epigenetic modifications, which are commonly microRNA guided. Employin...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9478-8
更新日期：2011-12-01 00:00:00
abstract：:Analysis of cDNAs from Macrovipera lebetina transmediterranea (Mlt) and Echis ocellatus (Eo) venom gland libraries encoding disintegrins argued strongly for a common ancestry of the messengers of short disintegrins and those for precursors of dimeric disintegrin chains. We now report the sequence analysis of disintegr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0161-4
更新日期：2007-02-01 00:00:00
abstract：:Studies so far have correlated the variation in the composition of snake venoms with the target prey population and snake's diet. Here we present the first example of an alternative evolutionary link between venom composition and dietary adaptation of snakes. We describe a dinucleotide deletion in the only three finge...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0138-0
更新日期：2005-01-01 00:00:00
abstract：:The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-017-9796-6
更新日期：2017-06-01 00:00:00
abstract：:Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosom...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0293-3
更新日期：2005-07-01 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：:In vitro run-off transcription by T7 RNA polymerase generates heterogeneous 3'-ends because the enzyme tends to add untemplated adenylates. To generate homogeneous 3'-termini, HDV ribozymes have been used widely. Their sequences are added to the 3'-terminus such that co-transcriptional self-cleavage generates homogene...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9861-9
更新日期：2018-08-01 00:00:00
abstract：:Insertions and deletions of entire codons have recently been discovered as a mechanism by which B cells, in addition to conventional base substitution, evolve the antibodies produced by their immunoglobulin genes. These events frequently seem to involve repetitive sequence motifs in the antibody-encoding genes, and it...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0049-2
更新日期：2002-03-01 00:00:00
abstract：:One crucial event during evolution to multicellularity was the development of either direct cell-cell contact or indirect interaction via extracellular matrix (ECM) molecules. The identification of those polypeptides provides conclusive data on the phylogenetic relationship of metazoan phyla and helps us to understand...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010230
更新日期：2001-10-01 00:00:00
abstract：:In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from the crystallographic structures, we performed all-atom molecular dynamics simulations and compare the traject...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-019-09894-4
更新日期：2019-07-01 00:00:00
abstract：:Males of three inbred lines of Drosophila melanogaster were heat-shocked 90 min at 37 degrees C. The progenies from treated and untreated males mated with untreated females of the same line were checked for their chromosomal insertion patterns of various mobile elements by either in situ hybridization or Southern blot...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02603073
更新日期：1989-05-01 00:00:00
abstract：:Computational and experimental attempts tried to characterize a universal core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiment...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0250-9
更新日期：2006-12-01 00:00:00
abstract：:MgtC is a virulence factor required for intramacrophage survival and growth in low Mg2+ medium in two pathogens that are not phylogenetically related, Salmonella typhimurium and Mycobacterium tuberculosis. In S. typhimurium, mgtC is carried by the SPI-3 pathogenicity island and hybridization studies have suggested tha...
journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/s00239-003-2496-4
更新日期：2003-10-01 00:00:00
abstract：:The transposable element mariner occurs widely in the melanogaster species group of Drosophila. However, in drosophilids outside of the melanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genus Zaprionus. The mariner sequence obtained from Zaprionus tuberculatus is...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102804
更新日期：1991-12-01 00:00:00
abstract：:Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subd...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2472-z
更新日期：2003-10-01 00:00:00
abstract：:Collagen is an important structural protein and the most abundant protein in mammals. In several research fields, structural analysis of collagens is performed. Fibrillar collagens almost entirely consist of continuous repeats of GXY, where G is glycine, X is often proline or alanine and Y is often hydroxyproline or a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9844-x
更新日期：2018-06-01 00:00:00
abstract：:The present work represents the first attempt to study in greater detail previously proposed compositional correlations in genomes, based on a body of additional data relating to gene localizations as well as to extended flanking sequences extracted from gene banks. We have investigated the correlations that exist bet...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102651
更新日期：1991-06-01 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
