The small non-coding RNA processing machinery of two living fossil species, lungfish and coelacanth, gives new insights into the evolution of the Argonaute protein family

Argonaute (AGO) family proteins play many roles in epigenetic programming, genome rearrangement, mRNA breakdown, inhibition of translation, and transposon silencing. Despite being a hotspot in current scientific research, their evolutionary history is still poorly understood and consequently the identification of evolutionary conserved structural features should also generate useful information for better understanding their functions. We report here for the first time the transcript sets of the two subfamilies, Ago and Piwi, in the West African lungfish Protopterus annectens and in the Indonesian coelacanth Latimeria menadoensis, two key species in the evolutionary lineage leading to tetrapods. The phylogenetic analysis of 142 inferred protein sequences in 22 fully sequenced species and the analysis of microsynteny performed in the major vertebrate lineages indicate an intricate pattern for the evolution of both subfamilies that has been shaped by whole genome duplications and lineage specific gains and losses. The argonaute subfamily was additionally expanded by local gene duplications at the base of the jawed vertebrate lineage. The subfamily of Piwi proteins is involved in several processes such as spermatogenesis, piRNA biogenesis, and transposon repression. Expression assessment of AGO genes and genes coding for proteins involved in small RNA biogenesis suggests a limited activity of the Piwi pathway in lungfish in agreement with the lungfish genome containing mainly old and inactive transposons

A study of osteological and molecular differences in populations of Aphanius fasciatus Nardo 1827, from the Central Mediterranean (Teleostei, Cyprinodontidae)

Nine populations of Aphanius fasciatus Nardo, 1827 from the central Mediterranean were analysed by examining the mitochondrial control region and the morphology of the bony elements of the skull and vertebral column, to study the degree of intraspecific differentiation of A. fasciatus considering the level of isolation of the different populations and the palaeogeographic history of the central Mediterranean area. Both the molecular and morphological analyses differentiate between the populations, even if the topologies of the two trees are different. Molecular and osteological investigations have consistently demonstrated a well-supported differentiation of the south-eastern Sicilian populations both within the same group (Tigano et al. in Ital J Zool 71:1124–1133, 2004a; Tigano et al. in Abstract volume XI European Congress of Ichthyology, Tallin, Estonia, 2004b), and from the populations from western Sicily, Tunisia and the island of Malta. The molecular results show that the nine populations are characterised by haplotypes that are well defined in relation to a probably limited gene flow; while, as regards the morphological data the differentiation found could be explained in terms of the geographic isolation of the various populations, although the influence of environmental factors, which differ greatly between the various sites where the populations live, cannot be ruled out.peer-reviewe

A comparative view on sex differentiation and gametogenesis genes in lungfish and coelacanths

none8siGonadal sex differentiation andreproductionare the keys totheperpetuationof favorable gene combinations andpositively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits sharedwith actinopterygians,which disappeared in the tetrapod lineage.openMaria Assunta Biscotti, Mateus Contar Adolfi, Marco Barucca, Mariko Forconi, Alberto Pallavicini, Marco Gerdol, Adriana Canapa, Manfred SchartlBiscotti, Maria Assunta; Contar Adolfi, Mateus; Barucca, Marco; Forconi, Mariko'; Pallavicini, Alberto; Gerdol, Marco; Canapa, Adriana; Schartl, Manfre

Karyological and genetic variation in Middle Eastern lacertid lizards, Lacerta laevis and the Lacerta kulzeri complex: a case of chromosomal allopatric speciation

Abstract Karyological (standard and C, Ag-NOR and Alu-I banding methods) and mtDNA analyses (cytochrome b and 12S rRNA) were conducted on specimens from eight allopatric populations of the Lacerta kulzeri complex. Parallel analyses were performed for comparison on Lacerta laevis specimens. Karyological and molecular studies support the morphological and ethological evidence indicating the speci¢c separation between Lacerta laevis and Lacerta kulzeri. In the Lacerta kulzeri complex, chromosomal analysis substantiated an interpopulation di¡erentiation roughly along a north^south trend, mainly regarding the sex chromosome morphology and heterochromatin. The cytochrome b and 12S rRNA gene analyses showed minor genetic di¡erences that were considerably smaller than those commonly found in genetically isolated populations. The L. kulzeri populations from Barouk, Druze and Hermon show a mean genetic distance that, in other saurians, characterises subspecies. The conditions found in L. laevis and L. kulzeri are reminiscent of King's model of chromosomal primary allopatry and support the hypothesis that in these lacertid lizards chromosome variations can become ¢xed before the accumulation of the genetic mutations

Analysis of the African coelacanth genome sheds light on tetrapod evolution

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution

An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality

Hox genes are regulators of animal embryonic development. Changes in the number and sequence of Hox genes as well as in their expression patterns have been related to the evolution of the body plan. Lophotrochozoa is a clade of Protostomia characterized by several phyla which show a wide morphological diversity. Despite that the works summarized in this review emphasize the fragmentary nature of the data available regarding the presence and expression of Hox genes, they also offer interesting insight into the evolution of the Hox cluster and the role played by Hox genes in several phyla. However, the number of genes involved in the cluster of the lophotrochozoan ancestor is still a question of debate. The data presented here suggest that at least nine genes were present while two other genes, Lox4 and Post-2, may either have been present in the ancestor or may have arisen as a result of duplication in the Brachiopoda-Mollusca-Annelida lineage. Spatial and temporal collinearity is a feature of Hox gene expression which was probably present in the ancestor of deuterostomes and protostomes. However, in Lophotrochozoa, it has been detected in only a few species belonging to Annelida and Mollusca

New insights into the genome repetitive fraction of the Antarctic bivalve Adamussium colbecki

Repetitive DNA represents the major component of the genome in both plant and animal species. It includes transposable elements (TEs), which are dispersed throughout the genome, and satellite DNAs (satDNAs), which are tandemly organized in long arrays. The study of the structure and organization of repetitive DNA contributes to our understanding of genome architecture and the mechanisms leading to its evolution. Molluscs represent one of the largest groups of invertebrates and include organisms with a wide variety of morphologies and lifestyles. To increase our knowledge of bivalves at the genome level, we analysed the Antarctic scallop Adamussium colbecki. The screening of the genomic library evidenced the presence of two novel satDNA elements and the CvA transposon. The interspecific investigation performed in this study demonstrated that one of the two satDNAs isolated in A. colbecki is widespread in polar molluscan species, indicating a possible link between repetitive DNA and abiotic factors. Moreover, the transcriptional activity of CvA and its presence in long-diverged bivalves suggests a possible role for this ancient element in shaping the genome architecture of this clade

Isolation of Hox and ParaHox genes in bivalve Pecten maximus.

The Hox cluster genes encode a set of transcription factors that have been shown to control spatial patterning mechanisms in bilaterian organism development. The ParaHox cluster is the evolutionary sister of the Hox cluster. The two are believed to descend from an ancestral ProtoHox cluster of four genes from which the three ParaHox genes (Gsx, Xlox, and Cdx) and the four Hox gene classes are believed to have originated. Although molluscs are among the most successful lophotrochozoan groups, very little work has been devoted to the characteristics of their homeotic genes. Using polymerase chain reaction-based approaches, we isolated 13 different Pecten maximus (Bivalvia: Pteriomorphia) sequences corresponding to all the genes of the four Hox cluster classes and to genes Xlox and Cdx of the ParaHox cluster. Comparison of results with those obtained in other lophotrochozoans seems to confirm the considerable homogeneity of the Hox and ParaHox genes in these taxa both as regards the presence of nearly all the genes of the two clusters and the marked sequence resemblance among orthologous genes. © 2005 Elsevier B.V. All rights reserved