A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

Background: The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results: We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion:The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.Additional co-authors: Thomas D Kocher, Catherine Ozouf-Costaz, Jean Francois Baroiller and Francis Galiber

Barcoding, molecular taxonomy, and exploration of the diversity of shrews (Soricomorpha: Soricidae) on Mount Nimba (Guinea)

International audienc

Contrasting Genetic Structure among Populations of Two Amphidromous Fish Species (Sicydiinae) in the Central West Pacific

Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9-0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (phi(ST) = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79-625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion

In Situ Gene Mapping of Two Genes Supports Independent Evolution of Sex Chromosomes in Cold-Adapted Antarctic Fish

Two genes, that is, 5S ribosomal sequences and antifreeze glycoprotein (AFGP) genes, were mapped onto chromosomes of eight Antarctic notothenioid fish possessing a X1X1X2X2/X1X2Y sex chromosome system, namely, Chionodraco hamatus and Pagetopsis macropterus (family Channichthyidae), Trematomus hansoni, T. newnesi, T. nicolai, T. lepidorhinus, and Pagothenia borchgrevinki (family Nototheniidae), and Artedidraco skottsbergi (family Artedidraconidae). Through fluorescence in situ hybridization (FISH), we uncovered distinct differences in the gene content of the Y chromosomes in the eight species, with C. hamatus and P. macropterus standing out among others in bearing 5S rDNA and AFGP sequences on their Y chromosomes, respectively. Both genes were absent from the Y chromosomes of any analyzed species. The distinct patterns of Y and non-Y chromosome association of the 5S rDNA and AFGP genes in species representing different Antarctic fish families support an independent origin of the sex heterochromosomes in notothenioids with interesting implications for the evolutionary/adaptational history of these fishes living in a cold-stable environment

Needlepoint non-destructive internal tissue sampling for precious fish specimens

International audienceIn this paper, we describe a new non-damaging internal tissue sampling method for preserved collection of teleostean specimens. It was tested on freshwater pipefish, as external tissue sampling is made difficult by the lack of scales, the lack of pelvic fins, the atrophy of pectoral and anal fins. The internal tissue is detached by scratching the inside of the urogenital papilla with a fine metallic probe. 95% ethanol is injected using a fine syringe, and then sucked back into the syringe with the detached tissue. This protocol has been tested on 6 specimens from 5 species of pipefish. For each specimen DNA was extracted from the internal tissue, a caudal fin clip, and when possible, eggs sampled from the male brooding pouch. Partial Cytochrome c oxydase I (COI) was amplified and sequenced. For each specimen, the 582 bp long sequences obtained from the internal tissue, the fin clip and the eggs were identical. These results validate this non-damaging internal tissue sampling method, which leaves absolutely no trace on the specimen. Although this method was developed on pipefish, it could be applied to other teleostean, even precious museum collection specimens such as type specimens. The aim of this paper, using the example of freshwater pipefish, is to present this method, which aims at preserving precious collection specimens while still valorising them

Biodiversity and phylogeny of Ammotheidae (Arthropoda: Pycnogonida)

The family Ammotheidae is the most diversified group of the class Pycnogonida, with 297 species described in 20 genera. Its monophyly and intergeneric relationships have been highly debated in previous studies. Here, we investigated the phylogeny of Ammotheidae using specimens from poorly studied areas. We sequenced the mitochondrial gene encoding the first subunit of cytochrome c oxidase (CO1) from 104 specimens. The complete nuclear 18S rRNA gene was sequenced from a selection of 80 taxa to provide further phylogenetic signal. The base composition in CO1 shows a higher heterogeneity in Ammotheidae than in other families, which may explain their apparent polyphyly in the CO1 tree. Although deeper nodes of the tree receive no statistical support, Ammotheidae was found to be monophyletic and divided into two clades, here defined as distinct subfamilies: Achelinae comprises the genera Achelia Hodge, 1864, Ammothella Verrill, 1900, Nymphopsis Haswell, 1884 and Tanystylum Miers, 1879; and Ammotheinae includes the genera Ammothea Leach, 1814, Acheliana Arnaud, 1971, Cilunculus Loman, 1908, Sericosura Fry & Hedgpeth, 1969 and also Teratonotum gen. nov., including so far only the type species Ammothella stauromata Child, 1982. The species Cilunculus gracilis Nakamura & Child, 1991 is reassigned to Ammothella, forming the binomen Ammothella gracilis (Nakamura & Child, 1991) comb. nov. Additional taxonomic re-arrangements are suggested for the genera Achelia, Acheliana, Ammothella and Cilunculus

Première estimation de l’évolution du caryotype chez les Mormyridae

International audienceThe chromosomal diversity within six species of Mormyridae belonging to six different genera (Gnathonemus petersii, Marcusenius moorii, Ivindomyrus obdenboschi, Brienomyrus sp., Stomatorhinus walkeri and Petrocephalus microphthalmus) is investigated for the first time. These species have a conserved diploid chromosome number of 2n = 50 (except G. petersii 2n = 48) but different chromosome formulae, essentially involving pericentric inversions. C-banding has been used for the localization of heterochromatin. For a deeper interspecific comparison, several molecular markers were localized in the chromosomes by fluorescence in situ hybridization (FISH): a 18S rDNA probe; a microsatellite probe (GAA)(10), and a telomeric probe (TTAGGG)(7). The distribution of the 18S rDNA patterns, in particular, shows an amazing specific diversity, confirming a rapid radiation accompanied by major chromosome rearrangements.La diversité chromosomique a été explorée pour la première fois parmi six espèces de Mormyridae appar-tenant à six genres différents (Gnathonemus petersii, Marcusenius moorii, Ivindomyrus obdenboschi, Brieno-myrus sp., Stomatorhinus walkeri and Petrocephalus microphthalmus). Ces espèces ont un nombre identique de chromosomes (2n = 50), à l’exception de G. petersii (2n = 48), mais des formules chromosomiques différentes, mettant essentiellement en jeu des inversions péricentriques. le marquage en bandes C a été utilisé pour localiser l’hétérochromatine. Pour une comparaison interspécifique plus approfondie, plusieurs marqueurs moléculaires ont été localisés dans les chromosomes par hybridation in situ en fluorescence (FISH) : une sonde ADN riboso-mique 18s; un microsatellite (gaa)10, et une sonde télomérique (ttaggg)7. la distribution chromosomique des signaux produits par la sonde ADNr 18S est particulièrement diversifiée parmi ces espèces, ce qui indique une radiation rapide accompagnée par des remaniements chromosomiques majeurs

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)

Garrigos, Yareli Esquer, Hugueny, Bernard, Koerner, Kellie, Ibañez, Carla, Bonillo, Celine, Pruvost, Patrice, Causse, Romain, Cruaud, Corinne, Gaubert, Philippe (2013): Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae). Zootaxa 3640 (3): 373-394, DOI: http://dx.doi.org/10.11646/zootaxa.3640.3.

First insights into karyotype evolution within the family Mormyridae

International audienceThe chromosomal diversity within six species of Mormyridae belonging to six different genera (Gnathonemus petersii, Marcusenius moorii, Ivindomyrus obdenboschi, Brienomyrus sp., Stomatorhinus walkeri and Petrocephalus microphthalmus) is investigated for the first time. These species have a conserved diploid chromosome number of 2n = 50 (except G. petersii 2n = 48) but different chromosome formulae, essentially involving pericentric inversions. C-banding has been used for the localization of heterochromatin. For a deeper interspecific comparison, several molecular markers were localized in the chromosomes by fluorescence in situ hybridization (FISH): a 18S rDNA probe; a microsatellite probe (GAA)(10), and a telomeric probe (TTAGGG)(7). The distribution of the 18S rDNA patterns, in particular, shows an amazing specific diversity, confirming a rapid radiation accompanied by major chromosome rearrangements

Fish et microdissection dans le cadre d'un projet d'étude de l'évolution du déterminisme du sexe sur les tilapia : chronique d'une stratégie de recherche en boucle

National audienceLes tilapias constituent d’excellents modèles pour l’étude de l’évolution du déterminisme du sexe et la différenciation des chromosomes. Des données récentes suggèrent que ce groupe d’espèces, se trouve à une période charnière de substitution d’une grande paire de chromosomes sexuels ZZ/ZW (Oreochromis aureus) par une petite paire, XX/XY (O. niloticus) via l’émergence d’un facteur mineur devenant progressivement le nouveau déterminant du sexe. En effet, à partir de la carte génétique d’O. niloticus, 2 groupes de liaison, LG1 et LG3, fortement liés au sexe, ont été identifiés chez le tilapia. Chez O. aureus, LG3, localisé par FISH sur la grande paire de chromosomes contient le déterminant majeur du sexe et LG1, localisé sur une petite paire, peut contenir, chez certaines familles/populations, un déterminant mineur du sexe. Inversement, chez O. niloticus, LG3 ne joue plus qu’un rôle mineur dans le déterminisme du sexe, alors que LG1 contient le déterminant majeur. Leurs structures (suppression de recombinaison, accumulation de séquences.répétées / rétrotransposons), suggèrent que ce sont respectivement un vieux et un jeune chromosomes sexuels. En s’appuyant sur des génotypes sexuels spécifiques (mâles et femelles XX, XY, et YY disponibles chez O. niloticus; mâles et femelles ZZ, ZW et femelles gynogénétiques WW à produire chez O. aureus), notre projet multi équipes (CIRAD-CNRS-INRA) cherche à isoler, par microdissection classique ou laser, les 4 paires de chromosomes sexuels des tilapias (X, Y, Z et W). La stratégie consiste à hybrider une source contenant une large quantité de gènes (ADNc) sur des préparations métaphasiques puis à microdisséquer les chromosome d’intérêt, après marquage par un BAC spécifique. Sur chacun de ces chromosomes microdisséqués et amplifiés par PCR, une hybridation directe des ADNc sera ensuite réalisée .afin d’identifier et d’isoler les gènes qui s’hybrident sur chacune des paires de chromosomes sexuels. Les gènes ainsi identifiés seront hybridés sur une banque de BACs et les BACs contenant ces gènes réhybridés sur les chromosomes de chaque génotype pour un ultime contrôle de leur localisation. Les équipes de cytogénétique impliquées dans le projet expliquent ici à quelles étapes elles interviennent (préparations chromosomiques, FISH, microdissection) quelle est leur contribution dans ce projet et quelles sont leurs stratégies pour surmonter les problèmes techniques posés