Insertion of a self-splicing intron into the mtDNA of atriploblastic animal

Nephtys longosetosa is a carnivorous polychaete worm that lives in the intertidal and subtidal zones with worldwide distribution (pleijel&rouse2001). Its mitochondrial genome has the characteristics typical of most metazoans: 37 genes; circular molecule; almost no intergenic sequence; and no significant gene rearrangements when compared to other annelid mtDNAs (booremoritz19981995). Ubiquitous features as small intergenic regions and lack of introns suggested that metazoan mtDNAs are under strong selective pressures to reduce their genome size allowing for faster replication requirements (booremoritz19981995Lynch2005). Yet, in 1996 two type I introns were found in the mtDNA of the basal metazoan Metridium senile (FigureX). Breaking a long-standing rule (absence of introns in metazoan mtDNA), this finding was later supported by the further presence of group I introns in other cnidarians. Interestingly, only the class Anthozoa within cnidarians seems to harbor such introns. Although several hundreds of triploblastic metazoan mtDNAs have been sequenced, this study is the first evidence of mitochondrial introns in triploblastic metazoans. The cox1 gene of N. longosetosa has an intron of almost 2 kbs in length. This finding represents as well the first instance of a group II intron (anthozoans harbor group I introns) in all metazoan lineages. Opposite trends are observed within plants, fungi and protist mtDNAs, where introns (both group I and II) and other non-coding sequences are widespread. Plant, fungal and protist mtDNA structure and organization differ enormously from that of metazoan mtDNA. Both, plant and fungal mtDNA are dynamic molecules that undergo high rates of recombination, contain long intergenic spacer regions and harbor both group I and group II introns. However, as metazoans they have a conserved gene content. Protists, on the other hand have a striking variation of gene content and introns that account for the genome size variation. In contrast to this mtDNA structure and organization diversity, current genome level studies point to a monophyletic origin of the mitochondria (REFS), raising questions such as: what are the pressures at work shaping the evolution of the mitochondrial genome at 'higher' levels? What drives the absence of introns and other non-coding spacers in metazoan mtDNA? What characteristics must have an intron to be maintained in an environment where 'extra chromosomes' are usually selected against

A framework for orthology assignment from gene rearrangement data

Abstract. Gene rearrangements have successfully been used in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive when comparing nuclear genomes. The main challenge is how to deal with gene families, specifically, how to identify orthologs. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. We approach that problem using gene rearrangement data, provide an optimization framework in which to phrase the problem, and present some preliminary theoretical results.

Synthesis of accelerograms compatible with the Chinese GB 50011-2001 design spectrum via harmonic wavelets: artificial and historic records

A versatile approach is employed to generate artificial accelerograms which satisfy the compatibility criteria prescribed by the Chinese aseismic code provisions GB 50011-2001. In particular, a frequency dependent peak factor derived by means of appropriate Monte Carlo analyses is introduced to relate the GB 50011-2001 design spectrum to a parametrically defined evolutionary power spectrum (EPS). Special attention is given to the definition of the frequency content of the EPS in order to accommodate the mathematical form of the aforementioned design spectrum. Further, a one-to-one relationship is established between the parameter controlling the time-varying intensity of the EPS and the effective strong ground motion duration. Subsequently, an efficient auto-regressive moving-average (ARMA) filtering technique is utilized to generate ensembles of non-stationary artificial accelerograms whose average response spectrum is in a close agreement with the considered design spectrum. Furthermore, a harmonic wavelet based iterative scheme is adopted to modify these artificial signals so that a close matching of the signals’ response spectra with the GB 50011-2001 design spectrum is achieved on an individual basis. This is also done for field recorded accelerograms pertaining to the May, 2008 Wenchuan seismic event. In the process, zero-phase high-pass filtering is performed to accomplish proper baseline correction of the acquired spectrum compatible artificial and field accelerograms. Numerical results are given in a tabulated format to expedite their use in practice

Relationships between hexapods and crustaceans based on 4 mitochondrial genes.

The ever-increasing use of molecular data in phylogenetic studies have revolutionized our view of the phylogenetic relationships among the major lineages of arthropods. In this context, an important contribution is offered by mitochondrial genes, and the now widely available sequences of entire mitochondrial genomes. One of the most debated issues in arthropod phylogeny is the relationship between crustaceans and hexapods, and particu- larly, whether the traditional taxa Crustacea and Hexapoda are mono- or paraphyletic. A key role is played by basal hexapodan taxa, the entognathan apterygotans (Protura, Collem- bola, Diplura), whose phylogenetic position as the sister taxa of the Insecta s. str. is not totally convincing. The phylogenetic analysis based on mitochondrial protein-coding genes suggests that there are crustacean taxa which are more closely related to the Insecta s. str. than Collembola and Diplura, therefore suggesting non-monophyly of the taxon Hexapoda as traditionally defined. Hence, Collembola and Diplura might have differentiated from different pancrustacean ancestor(s) than those from which the remaining hexapods (Insecta) arose. These results also imply a new scenario for the evolution of several morphological and physiological features of hexapods, including terrestrialization

The mitochondrial genomes of Campodea fragilis and C. lubbocki (Hexapoda: Diplura): high genetic divergence in a morphologically uniform taxon

Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions

The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda: Diplura): High genetic divergence in a morphologically uniform taxon

Complete mitochondrial genome sequences are presented from two dipluran hexapods (i.e., a group of “primarily wingless insects”) of the genus Campodea and compared to those of other arthropods. Their gene order is the same as in most other hexapods and crustaceans. Structural changes have occurred in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2 as well as in both ribosomal RNAs. These mtDNAs have striking biases in nucleotide and amino acid composition. Although the two Campodea species are morphologically highly similar, their genetic divergence is larger than expected, suggesting a long evolutionary history, perhaps under stable ecological condition