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The present paper describes AMmtDB, a database collecting the multi-aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs, as well as the multiple alignment of the mammalian mtDNA main regulatory region (D-loop) sequences. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. As far as the genes coding for tRNAs are concerned, the multi-alignments based on the primary and the secondary structures are both provided; for the mammalian D-loop multi-alignments we report the conserved regions of the entire D-loop (CSB1, CSB2, CSB3, the central region, ETAS1 and ETAS2) as defined by Sbisà et al. [ Gene (1997), 205, 125-140). A flatfile format for AMmtDB has been designed allowing its implementation in SRS (http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB ). Data selected through SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually.

Lectins are a class of defence proteins of non-immune origin that bind carbohydrate in a reversible fashion. In some cultivated legume species, lectin protein coding genes were PCR amplified using primers designed on the basis of conserved N- and C-terminal amino acid sequences of the common bean (one-chain) or pea (two-chains) lectins. Amplification products of the expected length were obtained in Lathyrus sativus L., Vicia faba L. var. faba, Phaseolus coccineus L., and Vigna unguiculata (L.) Walp. No amplification product or agglutinating activity against blood cells, and/or cross-reaction with specific antibodies were detected in Lupinus albus L. and Cicer arietinum L. Finally, the new isolated nucleotide sequences, together with other legume lectin sequences already present in the EMBL Database, were used for evolutionary analysis. This last indicated the existence of two main clusters; one grouping all the species belonging to the Phaseoleae tribe and the other one grouping Lens culinaris Medik., Pisum sativum L., L. sativus, and V. faba, members of the Vicieae tribe. Results were congruent with the taxonomic classification and suggested that the lectin genes divergence in legume followed species evolution.

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Root-knot nematodes belonging to the genus Meloidogyne constitute one of the major groups of plant pathogens of outstanding economic importance. They are facultative or obligate parthenogens, so a single individual can establish a population, a useful attribute in species that exploits disturbed ecosystems such as the agro-ecosystems. Molecular studies of root knot nematode ribosomal genes are undertaken both to elucidate their phylogenetic relationships and to develop DNA-based methods for their identification. Within the order Tylenchida, Meloidogyne artiellia 5S rRNA has a different location, with respect to other Meloidogyne species, but similar to that observed in the distantly related Caenorhabditis elegans, order Rhabditida. Moreover the availability of the complete sequence of the M. artiellia repeated ribosomal unit, allowed us to address phylogenetic relationships within the genus Meloidogyne. M. artiellia displays several characteristics, presumably present in the common ancestor, whose traces are still present in members of the different order Rhabditida, such as C. elegans, in spite of the extremely fast evolution of nematodes.

A fragment of the NSM gene of naturally occurring Tomato spotted wilt virus (TSWV) isolates recovered in Apulia (southern Italy) from different cultivated and wild plant species was amplified by RT-PCR. The resulting 670 bp amplicon was cloned, sequenced and compared with available NSM sequences of other tospoviruses. The primary nucleotide sequence was 94.3 to 100% identical in all the Apulian TSWV isolates and had a 94-99% identity with TSWV-BR01, TSWV-L3, TSWV-JP, TSWV-A and TSWV-D. With other tospoviruses, sequence identity was in the range of 81-83% with Tomato chlorotic spot virus and Chrysanthemum stem necrosis virus and, 74-79% with Groundnut ring spot virus, Zucchini lethal chlorosis virus and Impatiens necrotic spot virus, 53-55% with Iris yellow spot virus, Peanut bud necrosis virus and Watermelon silver mottle virus. The phylogenetic tree showed three primary branches departing from the bulk of all NSM sequences; all the TSWV sequences clustered in two subgroups, denoted A-like and D-like, clearly distinct from the other tospoviruses. The inclusion in a group of any of the Apulian isolates of TSWV was apparently not determined by the year, the place or the host from which they were recovered. The A-like isolates clustered with TSWV-A, an isolate that was able to overcome host and pathogen-mediated resistance in tomato whereas the remaining six isolates clustered with TSWV-D, an isolate that did not overcome these forms of resistance. A simple and rapid procedure based on RT-PCR followed by enzymatic digestion was developed to identify isolates of the two subgroups.

The AMmtDB database (http://bighost.area.ba.cnr.it/mitochondriome) has been updated by collecting the multi-aligned sequences of Chordata and Invertebrata mitochondrial genes coding for proteins and tRNAs. Links to the multi-aligned mtDNA intraspecies variants, collected in VarMmtDB at the Mitochondriome web site, have been introduced. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually.

Lectin-related polypeptides are a class of defence proteins found in seeds of Phaseolus species. In Lima bean (P. lunatus), these proteins and their genes have been well characterized in the Andean morphotype, which represents one of the two gene pools of this species. To study the molecular evolution of the lectin family in Lima bean we characterized the polypeptides belonging to this multigene family and cloned the genes belonging to the Mesoamerican gene pool. The latter gene pool contains components similar to those of the Andean pool, namely: an amylase inhibitor-like (AIL), an arcelin-like (ARL) lectin and the less abundant Lima bean lectin (LBL). These proteins originate from an ancestor gene of the lectin type which duplicated to yield the lectin gene and the progenitor of ARL and AIL. In this species. ARL represents an evolutionary intermediate form that precedes AIL. Phylogenetic analysis supports an Andean origin for Lima bean. The molecular evolutionary studies were extended to the genes of common bean and demonstrated that true lectin genes and the ancestor of lectin-related genes are the result of a duplication event that occurred before speciation. Lima and common bean followed different evolutionary pathways and in the latter species a second duplication event occurred that gave rise, in Mesoamerican wild genotypes, to arcelin genes.