RICERCA ITALIANA     

Mitochondrial genomics in different groups of Metazoa: molecular and structural evolution and phylogenetic usefulness of the mitochondrial genome

Università degli Studi di Siena

Abstract

This collaborative project will be centered on the evolution of the mitochondrial genome (mtDNA), and on its usefulness as a phylogeographic and phylogenetic marker at different taxonomic levels in different taxa of Metazoa. The project represents the collaborative effort of four Research Units (R.U.), led by young Principal Investigators, but all of them characterized a remarkable tradition of research on the evolution of mtDNA, and by an outstanding record of publications in the field of molecular evolution and the phylogenetic significance of mitochondrial DNA.
From a methodological standpoint, the main effort will be dedicated to the sequencing of complete mitochondrial genomes in selected taxa of bivalves, hexapods, fishes and reptiles. The approach to whole-genome sequencing will be common to all R.U. and will be based on the application of Long-PCR and shotgun sequences. The potential usefulness of the Rolling Circle Amplification will also be tested. The presence of a common methodological strategy will allow extensive integration and collaboration between the four R.U. involved in the project, as well as the possibility of exploiting common sophisticated equipment. About 50 new complete mitochondrial genomes will be sequenced, annotated, described and submitted to GenBank, to make them available to the whole scientific community.
Selected taxa will be sampled at different taxonomic levels, according to the aim of the phylogeographic/phylogenetic >>>

Principal Investigator

Francesco Frati Università degli Studi di SIENA

Research Objectives

The outstanding scientific records of the Principal Investigators of each Research Units (see section 14 and the relative B forms) guarantees for the possibility to achieve the ambitious scientific targets set by this collaborative project. The common research target of this collaborative project is the sequencing of entire mitochondrial genomes in selected species from different taxonomic lineages of Metazoa. Entire mitochondrial genomes will represent the basic data for inferring evolutionary relationships at different taxonomic levels (phylogeography and phylogeny), for elucidating the molecular mechanisms of inheritance of mitochondrial DNA (mtDNA), and for unravelling processes of local adaptation mediated by relaxed and/or directional selection.
The collaborative project is based on a large sequencing effort, aiming at obtaining the complete sequence of about 50 mitochondrial genomes, for a ground total of almost 1 Gb of sequence information. These sequences will cover a broad taxonomic range (mollusks, hexapods, fishes and reptiles), and different taxonomic levels. Conspecific individuals will be sequenced in the reptile species Geochelone elephantopus and Varanus komodoensis, while species from different families will be sequenced in the teleost suborder Notothenioidei. In the Bivalvia (Mollusca) and the Hexapoda (Arthropoda), individuals from different families, representing different orders, will be sequenced. Such an extensive data set will allow the >>>

First Results

As described in section 11, the present project is organized around eight main objectives. Two of them are typical phylogeographic studies, with special emphasis on island biogeography and conservational and management implications. Four objectives are typical phylogenetic studies, at different taxonomic levels (and age of the diversification events), in different taxa (Teleostei, Arthropoda and Bivalvia). One objective will deal with the mechanisms of inheritance of the mitochondrial genome in species of the Bivalvia showing the peculiar phenomenon of the Doubly Uniparental Inheritance of mtDNA. One objective will address the mechanisms and the consequences at the molecular level of the adaptation to the Antarctic extreme environment of a family of endemic teleosts.
In all instances, the principal interest of these research lines is represented by the advancement of the scientific knowledge on the different subjects, all of them being still highly controversial. But in the cases of the phylogeographic studies on the Galapagos giant tortoises, Geochelone elephantopus, and the Komodo dragon, Varanus komodoensis, their status of endangered species implies the likelihood that the data produced will represent a solid scientific background to support the planning of management strategies.
In the Galapagos giant tortoises, the comparison of the entire mitochondrial genomes will lead to draw an exhaustive picture of the relationships among the different subtaxa (races >>>

Timescale

24 months

National and international background

The mitochondrial genome (mtDNA) is a closed circular molecule which exhibits an extraordinary degree of structural conservation across Metazoa. With very few exceptions, the mtDNA has a size ranging from 15 to 20 kb, and contains 37 genes (Boore 1999). Thirteen genes (PCGs) encode for subunits of enzymes involved in oxidative phosphorylation; there are three subunits (I-III) of the cytochrome c oxidase (cox1, cox2 and cox3), 7 subunits of the NADH dehydrogenase (nad1, nad2, nad3, nad4, nad4L, nad5, nad6), two subunits of the ATPase (atp6 and atp8), and the gene encoding for the cytochrome b (cytb). All proteins are used within the mitochondrion, in conjunction with additional subunits encoded in the nuclear genome and transported into the organelle. Twenty-two genes encode for their 22 corresponding tRNAs, one for each amino acid (trnX), with the exception of Leu and Ser which have two tRNAs each. Two genes (rrnS, rrnL) encode for the small and large subunits of ribosomal RNAs (12S and 16S), which participate in the assembling of the mitochondrial ribosomes. Their presence, and the complete array of tRNAs, allow the translation of mitochondrial genes to be carried out within the mitochondrion, making the organelle independent with respect to protein synthesis.
The genome has a very compact organization, with intergenic non-coding spacers being very short (few nucleotides), or absent: in certain circumstances, the coding sequences of tRNA genes overlap with the coding >>>