Evaluation of Genetic Variability among Three Pistacia Species Using Internal Transcribed Spacer 1 (ITS1) Marker

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

Detection and variability analyses of CRISPR-like loci in the H. pylori genome

Helicobacter pylori 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

Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution

Ministerio de Ciencia e Innovacio´ n of Spain (project nos. AGL2009-09094 and RYC-2011-08653), the University of Granada (project no. PP2016- PIP13), and the Natural Science Foundation of Fujian Province, China (project nos. 2021J01142 and 2018J01606) for providing financial support for this research.Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.Departamento de Genética. Grupo BIO200. Facultad de Ciencias. Universidad de Granad

An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

[Background] The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies. [Results] A consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7 cM with low average intermarker distance (3.7 cM; ~2 Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed, although largely variable among linkage groups and chromosome regions. Comparative sequence analysis revealed large macrosyntenic patterns against model teleost genomes, significant hits decreasing from stickleback (54%) to zebrafish (20%). Comparative mapping supported particular chromosome rearrangements within Acanthopterygii and aided to assign unallocated markers to specific turbot linkage groups. [Conclusions] The new gene-enriched high-resolution turbot map represents a useful genomic tool for QTL identification, positional cloning strategies, and future genome assembling. This map showed large synteny conservation against model teleost genomes. Comparative genomics and data mining from landmarks will provide straightforward access to candidate genes, which will be the basis for genetic breeding programs and evolutionary studies in this species.This study was supported by the projects: Consolider Ingenio Aquagenomics (CSD200700002), Spanish Ministerio de Ciencia e Innovación (AGL2009-13273), and Xunta de Galicia local Government (09MMA011261PR). We are indebted to Lucía Insua, María Portela, Susana Sánchez, María López, Mónica Otero and Sonia Gómez for technical assistance. B.G. Pardo was supported by an Isidro Parga Pondal research fellowship from Xunta de Galicia (Spain)

A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis

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 testisEuropean Union's Horizon 2020 research and innovation programme under grant agreement (AQUA-FAANG). Grant Number: 81792. Junta de Andalucía-FEDER Grant. Grant Number: P20-00938. Spanish Ministry of Economy and Competitiveness, FEDER Grants. Grant Numbers: RTI2018-096847-B-C21, RTI2018-096847-B-C22S

Genetic Variation in Damaged Populations of Pistacia atlantica Desf.

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 e orts should be taken separately for each population

Characterization of the complete mitochondrial genome of the striped soldier shrimp, Plesionika edwardsii (Brandt, 1851) (Crustacea: Decapoda: Pandalidae), and comparison with other species of Caridea

This work was funded as part of a project of investigation, development, and innovation of the 2020 European Regional Development Fund program (B.BIO.678.UGR20) “Análisis genético de Plesionika edwardsii en poblaciones del Mar de Alborán (PLESIGEN)” (Genetic analysis of Plesionika edwardsii in populations of the Alborán Sea).The striped soldier shrimp, Plesionika edwardsii (Brandt, 1851) is a pandalid with economic value in the Mediterranean region. We have sequenced and assembled its complete mitochondrial genome, which is 15,956 bp in length and contains the same 37 genes found in most metazoan mitochondrial genomes. Its gene order and nucleotide content are similar to most of the caridean mitochondrial genomes. In the comparative analysis, however, we detected in other species changes in the gene order that could be mediated by the recombination of transfer RNA genes, as well as AT skew shifts that could indicate changes in the origins of replication. All protein-coding genes of the mitochondrial genome of P. edwardsii seem to be under purifying selection, although the differences in Ka:Ks ratios suggest a disparity in the mutational constraints of some genes. This genome also presents a 1,118 bp-long non-coding sequence that encompass the control region. We have been able to find a previously described conserved sequence block in this region and assess that it forms a stem-loop structure in different species of Pandalidae, which is a shared feature with the conserved sequence blocks described in the family Alvinocarididae. We also detected microsatellites in the control region of P. edwardsii and in other species of Pandalidae and minisatellites in Lysmata vittata (Stimpson, 1860) that can account for around 20% of the additional non-coding region of this species. The phylogenetic relationships of P. edwardsii with other pandalids were assessed by two analyses: one based on the complete mitochondrial sequences and another based only on the protein-coding genes. Our study, thus, contributes to the genomic resources available for P. edwardsii and expands the current biological knowledge about the mitochondrial genomes of other caridean species.Departamento de Genética. Grupo BIO200. Facultad de Ciencias. Universidad de Granad

A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis

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.Spanish Government 81792 P20-00938 RTI2018-096847-B-C21European Commission 81792Junta de Andalucia-FEDER Grant P20-00938Spanish GovernmentEuropean Commission RTI2018-096847-B-C21 RTI2018-096847-B- C22Ministry of Economy and CompetitivenessJunta de Andaluci

miR-430 microRNA Family in Fishes: Molecular Characterization and Evolution

This research was funded by the Spanish Ministry of Economy and Competitiveness, FEDER, grant number RTI2018-096847-B-C22, and Regional Government of Andalusia—FEDER Grant: P20-00938.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.Departamento de Genética. Grupo BIO200. Facultad de Ciencias. Universidad de Granad