The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): considerable economization in the length and structural features of encoded genes.

Abstract:

:The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present.

journal_name

J Mol Evol

authors

He Y,Jones J,Armstrong M,Lamberti F,Moens M

doi

10.1007/s00239-005-0102-7

keywords:

subject

Has Abstract

pub_date

2005-12-01 00:00:00

pages

819-33

issue

6

eissn

0022-2844

issn

1432-1432

journal_volume

61

pub_type

杂志文章
  • Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes.

    abstract::Microsporidia are unicellular eukaryotes living as obligate intracellular parasites. Lacking mitochondria, they were initially considered as having diverged before the endosymbiosis at the origin of mitochondria. That microsporidia were primitively amitochondriate was first questioned by the discovery of microsporidia...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-004-2673-0

    authors: Thomarat F,Vivarès CP,Gouy M

    更新日期:2004-12-01 00:00:00

  • Conserved Critical Evolutionary Gene Structures in Orthologs.

    abstract::Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that mi...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-019-09889-1

    authors: Fuertes MA,Rodrigo JR,Alonso C

    更新日期:2019-04-01 00:00:00

  • Gypsy homologous sequences in Drosophila subobscura (gypsyDS).

    abstract::Characterization of sequences homologous to the Drosophila melanogaster gypsy transposable element was carried out in Drosophila subobscura (gypsyDS). They were found to be widely distributed among natural populations of this species. From Southern blot and in situ analyses, these sequences appear to be mobile in this...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF00166248

    authors: Alberola TM,de Frutos R

    更新日期:1993-02-01 00:00:00

  • Species specificity of bacterial palindromic units.

    abstract::We described previously a family of dispersed palindromic sequences highly repeated in Escherichia coli and Salmonella typhimurium genomes. These sequences, called PU (palindromic units), are located outside structural genes. We report here observations suggesting that PU may have a role in bacterial speciation. ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02603122

    authors: Gilson E,Perrin D,Saurin W,Hofnung M

    更新日期:1987-01-01 00:00:00

  • Autocatalytic Sets and RNA Secondary Structure.

    abstract::The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel computational model of chemical reaction networks based on RNA secondary structure and a...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-017-9787-7

    authors: Hordijk W

    更新日期:2017-04-01 00:00:00

  • Phylogenetic differences in content and intensity of periodic proteins.

    abstract::Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-squared-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 sp...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-004-0189-2

    authors: Gatherer D,McEwan NR

    更新日期:2005-04-01 00:00:00

  • Introducing intron locus cox1i624 for phylogenetic analyses in Bryophytes: on the issue of Takakia as sister genus to all other extant mosses.

    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

    authors: Volkmar U,Knoop V

    更新日期:2010-05-01 00:00:00

  • Detecting site-specific biochemical constraints through substitution mapping.

    abstract::The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-008-9139-8

    authors: Dutheil J

    更新日期:2008-09-01 00:00:00

  • Conserved organization of an avian histone gene cluster with inverted duplications of H3 and H4 genes.

    abstract::The organization of histone gene clusters of the duck Cairina moschata was studied in the DNA inserts of two recombinant phage that overlap and feature identical histone gene arrangements but differ in sequence details and in the extent of repetition of an AT-rich motif in one of the nontranscribed spacer regions. The...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02102477

    authors: Tönjes R,Munk K,Doenecke D

    更新日期:1989-03-01 00:00:00

  • Average values of a dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a computer-generated model system.

    abstract::Three measures of sequence dissimilarity have been compared on a computer-generated model system in which substitutions in random sequences were made at randomly selected sites and the replacement character was chosen at random from the set of characters different from the original occupant of the site. The three meas...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02602925

    authors: Blaisdell BE

    更新日期:1989-12-01 00:00:00

  • The catalysis of nucleotide polymerization by compounds of divalent lead.

    abstract::Soluble lead salts and a number of lead-containing minerals catalyze the formation of oligonucleotides from nucleoside 5'-phosphorimidazolides. The effectiveness of lead compounds correlates strongly with their solubility. Under optimal conditions we were able to obtain 18% of pentamer and higher oligomers from ImpA. ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF01732030

    authors: Sleeper HL,Orgel LE

    更新日期:1979-04-12 00:00:00

  • Self complementarity in messenger RNA of collagen. I. Possible hairpin structures in regions coding for oligopeptides of glycine, proline (hydroxyproline) and alanine.

    abstract::The periodic protein collagen is of special interest for the study of the relationship which exists between the structure of a protein and that of its mRNA, because oligopeptides containing glycine, proline (hydroxyproline) and alanine occur with great frequency in it. Collagen is particularly rich in these amino acid...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF01739101

    authors: Bachra BN

    更新日期:1976-08-03 00:00:00

  • A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13.

    abstract::The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-008-9156-7

    authors: Kohlsdorf T,Cummings MP,Lynch VJ,Stopper GF,Takahashi K,Wagner GP

    更新日期:2008-12-01 00:00:00

  • Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene.

    abstract::The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall e...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF00173421

    authors: Cao Y,Adachi J,Janke A,Pääbo S,Hasegawa M

    更新日期:1994-11-01 00:00:00

  • Evolution of the autosomal chorion cluster in Drosophila. IV. The Hawaiian Drosophila: rapid protein evolution and constancy in the rate of DNA divergence.

    abstract::Autosomal chorion genes s18, s15, and s19 are shown to diverge at extremely rapid rates in closely related taxa of Hawaiian Drosophila. Their nucleotide divergence rates are at least as fast as those of intergenic regions that are known to evolve more extensively between distantly related species. Their amino acid div...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02106055

    authors: Martínez-Cruzado JC

    更新日期:1990-11-01 00:00:00

  • Different rates of LINE-1 (L1) retrotransposon amplification and evolution in New World monkeys.

    abstract::LINE-1 (L1) elements constitute the major family of retrotransposons in mammalian genomes. Here we report the first investigation of L1 evolution in New World monkeys (NWM). Two regions of the second open-reading frame were analyzed by two methods in three NWM species, the squirrel monkey (Saimiri sciureus), the tamar...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-003-2539-x

    authors: Boissinot S,Roos C,Furano AV

    更新日期:2004-01-01 00:00:00

  • Exchanges of short polymorphic DNA segments predating speciation in feline major histocompatibility complex class I genes.

    abstract::Sequence comparisons of 14 distinct MHC class I cDNA clones isolated from species representing the three major taxonomic lineages of Felidae (domestic cat lineage, ocelot lineage, and pantherine lineage) revealed that feline MHC class I alleles have highly mosaic structures with short polymorphic sequence motifs that ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF00178246

    authors: Yuhki N,O'Brien SJ

    更新日期:1994-07-01 00:00:00

  • An estimate of divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata by aldolase and triose phosphate isomerase clocks.

    abstract::Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary di...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/pl00006208

    authors: Nikoh N,Iwabe N,Kuma K,Ohno M,Sugiyama T,Watanabe Y,Yasui K,Shi-cui Z,Hori K,Shimura Y,Miyata T

    更新日期:1997-07-01 00:00:00

  • Phylogeny of Nematoda and Cephalorhyncha derived from 18S rDNA.

    abstract::Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the closest to the coelomate animals. When phylogenetic trees were generat...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/pl00006416

    authors: Aleshin VV,Milyutina IA,Kedrova OS,Vladychenskaya NS,Petrov NB

    更新日期:1998-11-01 00:00:00

  • Evidence for positive selection on a sexual reproduction gene in the diatom genus Thalassiosira (Bacillariophyta).

    abstract::Single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL), and several random effects likelihood (REL) methods were utilized to identify positively and negatively selected sites in sexually induced gene 1 (Sig1) of four different Thalassiosira species. The SLAC analysis did not find any sites affected...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-006-0016-z

    authors: Sorhannus U,Kosakovsky Pond SL

    更新日期:2006-08-01 00:00:00

  • Trends in codon and amino acid usage in Thermotoga maritima.

    abstract::The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synon...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-001-0040-y

    authors: Zavala A,Naya H,Romero H,Musto H

    更新日期:2002-05-01 00:00:00

  • DNA microenvironments and the molecular clock.

    abstract::A few years ago we presented a stationary Markov model of gene evolution according to which only homologous genes from not too divergent species obeying the condition of being stationary may behave as reliable molecular clocks. A compartmentalized model of the nuclear genome in which the genes are distributed in compa...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02602910

    authors: Saccone C,Pesole G,Preparata G

    更新日期:1989-11-01 00:00:00

  • Dosage Compensation and the Distribution of Sex-Biased Gene Expression in Drosophila: Considerations and Genomic Constraints.

    abstract::Several studies in Drosophila have shown a paucity of male-biased genes (i.e., genes that express higher in males than in females) on the X chromosome. Dosage compensation (DC) is a regulatory mechanism of gene expression triggered in males that hypertranscribes the X-linked genes to the level of transcription in fema...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-016-9735-y

    authors: Gallach M,Betrán E

    更新日期:2016-05-01 00:00:00

  • Evolution of Alu family repeats since the divergence of human and chimpanzee.

    abstract::The DNA sequences of three members of the Alu family of repeated sequences located 5' to the chimpanzee alpha 2 gene have been determined. The base sequences of the three corresponding human Alu family repeats have been previously determined, permitting the comparison of identical Alu family members in human and chimp...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02115687

    authors: Sawada I,Willard C,Shen CK,Chapman B,Wilson AC,Schmid CW

    更新日期:1985-01-01 00:00:00

  • Comparative nucleotide diversity across North American and European populus species.

    abstract::Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. N...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-012-9504-5

    authors: Ismail M,Soolanayakanahally RY,Ingvarsson PK,Guy RD,Jansson S,Silim SN,El-Kassaby YA

    更新日期:2012-06-01 00:00:00

  • Rapid evolution in a fraction of the Drosophila nuclear genome.

    abstract::Previous observations have indicated that Drosophila DNA contains a component that evolves so rapidly that it fails to hybridize between the DNAs of sibling species. To establish the reality of this component and study its properties, the fraction (about 20%) of Drosophila simulans (Dsim) DNA that fails to hybridize t...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02099998

    authors: Werman SD,Davidson EH,Britten RJ

    更新日期:1990-03-01 00:00:00

  • Adhesive protein cDNA sequence of the mussel Mytilus coruscus and its evolutionary implications.

    abstract::cDNA encoding the adhesive protein of the mussel Mytilus coruscus (Mcfp1) was isolated. The coding region encoded 848 amino acids (a.a.) comprising the 20-a.a. signal peptide, the 21-a.a. nonrepetitive linker, and the 805-a.a. repetitive domain. Although the first 204 nucleotides and the 3'-untranslated region of Mcfp...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02339009

    authors: Inoue K,Takeuchi Y,Takeyama S,Yamaha E,Yamazaki F,Odo S,Harayama S

    更新日期:1996-10-01 00:00:00

  • Comparative molecular evolution of primary (Buchnera) and secondary symbionts of aphids based on two protein-coding genes.

    abstract::A+T content, phylogenetic relationships, codon usage, evolutionary rates, and ratio of synonymous versus non-synonymous substitutions have been studied in partial sequences of the atpD and aroQ/pheA genes of primary ( Buchnera) and secondary symbionts of aphids and a set of selected non-symbiotic bacteria, belonging t...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-001-2307-8

    authors: Moya A,Latorre A,Sabater-Muñoz B,Silva FJ

    更新日期:2002-08-01 00:00:00

  • The photolytic degradation and oxidation of organic compounds under simulated Martian conditions.

    abstract::Cosmochemical considerations suggest various potential sources for the accumulation of organic matter on Mars. However the Viking Molecular Analysis did not indicate any indigenous organic compounds on the surface of Mars. Their disappearance from the top layer is most likely caused by the combined action of the high ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF01732374

    authors: Oró J,Holzer G

    更新日期:1979-12-01 00:00:00

  • Duplication and diversification of the apolipoprotein CI (APOCI) genomic segment in association with retroelements.

    abstract::We have previously shown that several multicopy gene families within the major histocompatibility complex (MHC) arose from a process of segmental duplication. It has also been observed that retroelements play a role in generating diversity within these duplicated segments. The objective of this study was to compare th...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s002399910042

    authors: Freitas EM,Gaudieri S,Zhang WJ,Kulski JK,van Bockxmeer FM,Christiansen FT,Dawkins RL

    更新日期:2000-04-01 00:00:00