Genes involved in sex determination and differentiation have been identified in mice, humans, chickens, reptiles, amphibians and teleost fishes. However, little is known of their functional conservation, and it is unclear whether there is a common set of genes shared by all vertebrates. Coelacanths, basal Sarcopterygians and unique “living fossils”, could help establish an inventory of the ancestral genes involved in these important developmental processes and provide insights into their components. In this study 33 genes from the genome of Latimeria chalumnae and from the liver and testis transcriptomes of Latimeria menadoensis, implicated in sex determination and differentiation, were identified and characterized and their expression levels measured.Interesting findings were obtained for GSDF, previously identified only in teleosts and now characterized for the first time in the sarcopterygian lineage; FGF9, which is not found in teleosts; and DMRT1, whose expression in adult gonads has recently been related to maintenance of sexual identity. The gene repertoire and testis-specific gene expression documented in coelacanths demonstrate a greater similarity to modern fishes and point to unexpected changes in the gene regulatory network governing sexual development.

This study represents a preliminary systematic reorganization of the critical whip black coral genus Stichopathes from Indonesia, and a validation test of its principal morphological features as suitable taxonomic characters. A phylogenetic analysis based on rDNA internal transcribed spacer sequences ITS1 and ITS2 was performed on several specimens coming from different areas of the Indonesian Archipelago. Within the family Antipathidae, these analyses confirmed the separation of the three traditional genera of whip black corals (Stichopathes, Cirrhipathes, and Pseudocirrhipathes). Additionally, the analyses identified five clades for the studied Stichopathes specimens. In each clade, the wire specimens were well characterized by a distinctive set of morphological features, including: the shape of the corallum, the size and arrangement of the polyps, and the shape of the spines. The molecular data obtained, combined with other sequences available in the literature, indicate that the traditional genus Stichopathes is a polyphyletic taxon. In three clades, unbranched Stichopathes-like specimens group together with branched specimens morphologically belonging to the genus Antipathes. This evidence suggests caution when using the corallum branching pattern in the taxonomy of the order, as this character may have evolved separately in different taxa, thus suggesting that an extensive taxonomic revision of the whip black coral genera is required.

BackgroundLatimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species.ResultsThe deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.The RNA-seq analysis revealed remarkable differences in the expression profiles between the two tissues, allowing the identification of liver- and testis-specific transcripts which may play a fundamental role in important biological processes carried out by these two organs.ConclusionGiven the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.

Sponges are key components of the benthic assemblages and play an important functional role in many ecosystems, especially in coral reefs. The Indonesian coral reefs, located within the so-called “coral triangle”, are among the richest in the world. However, the knowledge of the diversity of sponges and several other marine taxa is far from being complete in the area. In spite of this great biodiversity, most of the information on Indonesian sponges is scattered in old and fragmented literature and comprehensive data about their diversity are still lacking. In this paper, we report the presence of 94 species recorded during different research campaigns mainly from the Marine Park of Bunaken, North Sulawesi. Six species are new for science and seven represent new records for the area. Several others are very poorly known species, sometimes recorded for the second time after their description. For most species, besides field data and detailed descriptions, pictures in vivo are included. Moreover, two new symbiotic sponge associations are described.This work aims to increase the basic knowledge of Indonesian sponge diversity as a prerequisite for monitoring and conservation of this valuable taxon.

No abstract