Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

This study was supported by the Spanish Ministry of Economy and Competitiveness, FEDER Grants (RTI2018-096847-B-C21 and RTI2018-096847-B-C22), Junta de Andalucía-FEDER Grant (P20-00938).The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions.RTI2018-096847B-C21 AND RTI2018-096847-B-C22 SPANISH MINISTRY OF ECONOMY AND COMPETITIVENESS -FEDE

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

Determinig the Specific Status of the Iberian Sturgeons by Means Genetic Analyses of Old Specimens

To clarify the species status of sturgeon from rivers of the Iberian Peninsula, eight molecular markers (4 nuclear and 4 mitochondrial) have been analysed in different specimens from historical museum samples and prehistoric samples from archaeological sites. These analyses indicate that one of these specimens (UGP captured in the Guadalquivir River in the 19th century) is A. sturio, based on all the eight molecular markers, four of them used from the first time in this study. In previous analyses based on 5 genetic markers, our group assigned two specimens captured in this river in the 1970-80s (EBD8173 and EBD8401) to the species A. naccarii, suggesting the presence of this species in the Iberian Peninsula. In this work, this conclusion is drawn after successfully obtaining a mitochondrial marker in a very old scute from a prehistoric site (Acinipo, about 1500 BC, from the Guadalquivir River basin). On the other hand, in the specimen EBD8174 captured in the Guadalquivir in 1975, we have obtained two new mitochondrial markers confirming that it can be considered A. sturio for all the mitochondrial markers, but nuclear ones identify it as A. naccarii. Finally, two very old samples (Nerja E-VI and Nerja N/62-63) were not successfully characterized by any molecular markers. Some aspects and consequences of our results are discussed, such as the origin of the “mosaic” specimen EBD8174 and, above all, the native status of A. naccarii in historic and prehistoric times in the southern Iberian Peninsula

Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5-9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions

Análisis de la variabilidad genética de Muscari Comosum L. (Liliaceae)

Universidad de Granada. Departamento de Genética. Leída el 3 de febrero de 198

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

Report on the 6th Genomics in Aquaculture (GIA) Symposium Held in Granada, Spain, 4–6 May 2022

Infectious diseases represent one of the most pressing threats to modern aquaculture at a global scale [...