Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal ...life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long‐ and short‐read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC‐FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post‐fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y‐linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X‐linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Diversity in Pistacia has been evaluated at all molecular levels using the internal transcribed spacer 1 (ITS1) marker in three species (Pistacia atlantica subsp. atlantica; Pistacia vera and ...Pistacia terebinthus), and compared with other Pistacia species. Results showed that the ITS amplification and sequencing, followed by phylogenetic analyses, identify the species and confirm their classification, which revealed that it can be used as a marker. Our results suggest that ITS1 analyses might provide a simple and inexpensive approach to validate the species of samples collected from the natural population, where species identification can be difficult, especially if hybrids are present or if the season is not optimal for identifying differences in morphological traits.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The miR-430 microRNA family has been described in multiple fish species as one of the first microRNAs expressed by the zygote. It has been suggested that this family is implicated in maternal mRNA ...elimination, but may also play a role in steroidogenesis, sexual differentiation, and flatfish metamorphosis. The miR-430 sequences have been found in multiple-copy tandem clusters but evidence of their conservation outside of teleost fishes is scarce. In the present study, we have characterized the tandem repeats organization of these microRNAs in different fish species, both model and of interest in aquaculture. A phylogenetic analysis of this family has allowed us to identify that the miR-430 duplication, which took place before the Chondrostei and Neopterygii groups' divergence, has resulted in three variants ("a", "b", and "c"). According to our data, variant "b" is the most closely related to the ancestral sequence. Furthermore, we have detected isolated instances of the miR-430 repeat subunit in some species, which suggests that this microRNA family may be affected by DNA rearrangements. This study provides new data about the abundance, variability, and organization of the miR-430 family in fishes.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this ...work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ ...hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176-178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Atlas Pistachio tree, Pistacia atlantica Desf., has great importance in the ecological landscape of North Africa, due to its adaptive plasticity, as well as its use as a rootstock in the ...cultivation of the economically important species, Pistacia vera L. The conservation and valuation of this species require sampling and an assessment of its genetic variability. For the first time in North Africa, the inter-simple sequence repeats (ISSR) molecular marker has been used in genetic-diversity assessment and in the population relationships of P. atlantica subsp. atlantica. The ISSR markers tested showed 74.1% polymorphism, while molecular variance (AMOVA) analysis revealed a high percentage of the total genetic diversity of 55.7% among the four populations studied. Cluster analysis with neighbor-joining (NJ) and principal coordinate analysis (PCO) divided the study sites into four distinct groups according to their geographical locations (Tiaret, Batna, Djelfa, and Bechar). Isolation by distance or Mantel test gave a positive correlation of r = 0.86 between geographical and genetic distances. The results in this study indicate an absence of gene flow, implying that conservation efforts should be taken separately for each population.
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•Purification of sperm using the “swim up” method.•Detection of OsHV-1 in sperm and oocytes of Crassostrea angulata.•Detection of OsHV-1 in 3day old larvae from 9 C. angulata full-sib ...families.•Vertical transmission of OsHV-1 in C. angulata that survived a mortality outbreak.
In order to determine if ostreid herpesvirus 1 (OsHV-1) can be vertically transmitted, 9 full-sib families of the Portuguese oyster Crassostrea angulata were produced using a factorial mating design with 3 males and 3 females. The parents were survivors from an OsHV-1 mortality outbreak. OsHV-1 DNA was not detected by conventional PCR in the mantle of parents, gametes or 3day-old larvae. However, viral DNA was detected by real-time PCR in all gametes and larvae samples. These results show that C. angulata that have survived an OsHV-1 mortality outbreak can carry the virus and vertically transmit it to their offspring.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Two new centromeric satellite DNAs in flatfish (Order Pleuronectiformes) have been characterized. The SacI-family from Hippoglossus hippoglossus, restricted to this species, had a monomeric size of ...334 base pair (bp) and was located in most of the centromeres of its karyotype. The PvuII-family, with a monomeric size of 177 bp, was initially isolated from the genome of Solea senegalensis, and fluorescent in situ hybridization (FISH) localized the repeat to centromeres of most of the chromosomes. This family could only be amplified in 2 other species of the genus Solea (Solea solea and Solea lascaris). Molecular features and chromosomal location indicated a possible structural and/or functional role of these sequence repeats. The presence of species-specific satellite-DNA families in the centromeres and their possible role in the speciation processes in this group of fishes is discussed.
An expressed sequence tag (EST) turbot database from immune tissues was tracked to identify and validate single nucleotide polymorphism (SNP) markers suitable for map construction and population ...analysis in turbot (
Scophthalmus maximus). By means of a stringent bioinformatic tracking strategy, 341 contigs containing true SNPs were identified among the 1827 existing in the database. The number of true SNPs per contig ranged between one and 20 for most contigs analyzed. However, some contigs showed higher numbers (many of them presumed artifactual SNPs), as a result of the bioinformatics workflow used for database construction and SNP searching. Two hundred and four contigs containing between one and nine SNPs or representing genes of special relevance were included for validation. Seventy-seven out of 166 SNPs that were successfully amplified resulted polymorphic and were combined in multiplexes for high-throughput genotyping. A total of 47 transitions, 28 transversions and two indels were detected among polymorphic SNPs, C/T being the commonest (34) and G/T the least common (4) substitutions observed. This represented a transition/transversion ratio of 1.885, similar to that observed in other fish studies. Minimum Allele Frequencies of the 77 polymorphic SNPs ranged from 0.031 to 0.500 (mean: 0.228
±
0.015) and unbiased expected heterozygosity (He) from 0.063 to 0.529 (mean: 0.329
±
0.016). Only two SNP loci deviated from Hardy–Weinberg expectations and no pair of loci deviated from random genotypic associations after correction for multiple tests. Analysis of segregation in eight large turbot families showed that only four loci deviated from Mendelian segregation after Bonferroni correction. The same analysis detected the presence of null alleles at two SNPs in accordance with the high frequency of null alleles estimated at these loci from population data. Fifteen contigs containing polymorphic SNPs (19.5%) could not be annotated after screening public databases with AutoFACT. Among those annotated, 43 (55.8%) were located in the 3′ untranslated region and 19 (24.7%) in the coding region, nine representing synonymous and 10 non-synonymous substitutions. Most of these genes appeared related to immune response and constitute candidates for functional changes in the correspondent proteins leading to putative phenotypic changes. These SNPs are the first validated in
Scophthalmus maximus, a species of high aquaculture relevance, and provide new genetic tools for genetic mapping and QTL identification, and for population structure and parentage analysis.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The genus Rumex includes hermaphroditic, polygamous, gynodioecious, monoecious, and dioecious species, with the dioecious species being represented by different sex-determining mechanisms and ...sex-chromosome systems. Therefore, this genus represents an exceptional case study to test several hypotheses concerning the evolution of both mating systems and the genetic control of sex determination in plants. Here, we compare nuclear intergenic transcribed spacers and chloroplast intergenic sequences of 31 species of Rumex. Our phylogenetic analysis supports a systematic classification of the genus, which differs from that currently accepted. In contrast to the current view, this new phylogeny suggests a common origin for all Eurasian and American dioecious species of Rumex, with gynodioecy as an intermediate state on the way to dioecy. Our results support the contention that sex determination based on the balance between the number of X chromosomes and the number of autosomes (X/A balance) has evolved secondarily from male-determining Y mechanisms and that multiple sex-chromosome systems, XX/XY1Y2, were derived twice from an XX/XY system. The resulting phylogeny is consistent with a classification of Rumex species according to their basic chromosome number, implying that the evolution of Rumex species might have followed a process of chromosomal reduction from x = 10 toward x = 7 through intermediate stages (x = 9 and x = 8).
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