Using Excel Mapper to Design Chromosome Idiograms

Idiograms are graphical representations in which chromosomes appear ordered by their relative size, homology groups, and the presence of cytogenetic landmarks such as centromeres, secondary constrictions, and banding patterns. They have become crucial elements in cytogenetic research. Here, we describe a simple protocol for spreadsheet software to draw idiograms and map any type of sequence onto them. These graphs can be easily used to present research results and can become the basis to raise and resolve questions related to different biological issues. The methodology is inexpensive, easy to follow, and allows customization to meet a wide range of educational scenarios focused in genetics and evolution.University of Granada PID-16-0

A Gene Calculator to teach mendelism, gene interaction and linkage

La Genética Mendeliana representa el primer contacto de los estudiantes con la Genética. Aunque es fundamental para entender las bases de la herencia, no recoge dos de las grandes excepciones que se producen en la naturaleza y que alteran las proporciones mendelianas: (1) las interacciones génicas, o la acción de varios genes que contribuyen a un mismo fenotipo y (2) el ligamiento genético, o la localización de varios genes en un mismo cromosoma. En este contexto, presentamos una herramienta web denominada Calculadora de Genes que permite profundizar en ambos aspectos. Por un lado, simula cruzamientos no solo de rasgos mendelianos tradicionales, sino también de rasgos con todos los tipos de interacciones génicas existentes. Por otro lado, permite estudiar el efecto del ligamiento en las proporciones mendelianas, haciendo estimas de distancias genéticas y ofreciendo una salida con la representación gráfica de los gametos que produciría un individuo que porta varios genes ligados. Analizamos el potencial educativo de esta herramienta y proponemos una actividad práctica para su aplicación en el aula.Mendelian Genetics represents the student’s gateway to Genetics. Although it is essential to understand the basis of inheritance, it does not include two important exceptions occurring in nature that distort Mendelian ratios: (1) gene interactions, or the joint action of several genes contributing to the same phenotype and (2) genetic linkage, or the location of several genes on the same chromosome. On these grounds, we present the Gene Calculator, a web tool that allows us to delve into both aspects. On the one hand, it simulates genetic crossings not only of traditional Mendelian traits but also of traits with all types of existing gene interactions. On the other hand, it allows studying the effect of linkage on Mendelian ratios by estimating genetic distances and generating an output with the graphic representation of the gametes produced by an individual with several linked genes. Finally, we evaluate the educational potential of this tool by proposing a practical activity to be used in the classroom

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

The genomic study of repetitive elements in Solea senegalensis reveals multiple impacts of transposable elements in the evolution and architecture of Pleuronectiformes chromosomes

Pleuronectiformes are flatfishes with high commercial value and a prominent example of successful marine adaptation through chromosomal evolution. Hence, the aim of this study was to analyze the 14 relative abundance of repetitive elements (satellite DNA and transposable elements (TE)) in the 15 genome of 10 fish species (8 flatfish) delving into the study of the species of special relevance, 16 Senegalese sole, Solea senegalensis. The results showed differences in the abundance of repetitive elements, with S. senegalensis exhibiting the highest frequency and coverage of these elements reaching the 40% of the genome and not at random distribution. It is noteworthy the presence of relevant peaks of Helitrons in centromeric/pericentromeric positions mainly in the bi-armed chromosomes 1, 2, 4, 6, 7, and 9. The position of the centromeres of this species determined through the genomic localization of the family of satellite DNA PvuII, and other repetitive sequences was obtained de novo. This allowed us to know the genomic position of the centromeres in 19 out of the 21 chromosomes of S. senegalensis. Helitrons showed an accumulation of tandem copies mainly in the pericentromeric positions of chromosomes 1 and 2, occupying a region, in the first case, of 600Kb of tandem repeats. That has only been previously described in mammals and plants. Divergence and copy number studies indicated the presence of active families in the species’ genome and the existence of two important events of transposon activity (burst) in the genome of S. senegalensis, mainly accentuated in Helitrons. The results showed that only the families of DNA transposons exhibited a landscape with symmetrical bell-shaped distribution. The phylogenetic analysis of Helitron families revealed the presence of two large groups of families and the presence of four groups of sequences with heterogeneous distribution among chromosomes. Finally, the phylogenomic analysis of 8615 sequences belonging to Helitron insertions from 5 families of flatfish and two external species, allowed to classify the copies into nine groups of sequences with different levels of divergence and clusters, including some branches with distant phylogenetically species. The implications of this study will help to expand the knowledge of chromosome structure and evolution of these species

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

Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution

Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Y(h)). To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Y(h) chromosome (HSY) and its X counterpart, yielding an 8.1-megabase (Mb) HSY pseudomolecule, and a 3.5-Mb sequence for the corresponding X region. The HSY is larger than the X region, mostly due to retrotransposon insertions. The papaya HSY differs from the X region by two large-scale inversions, the first of which likely caused the recombination suppression between the X and Y(h) chromosomes, followed by numerous additional chromosomal rearrangements. Altogether, including the X and/or HSY regions, 124 transcription units were annotated, including 50 functional pairs present in both the X and HSY. Ten HSY genes had functional homologs elsewhere in the papaya autosomal regions, suggesting movement of genes onto the HSY, whereas the X region had none. Sequence divergence between 70 transcripts shared by the X and HSY revealed two evolutionary strata in the X chromosome, corresponding to the two inversions on the HSY, the older of which evolved about 7.0 million years ago. Gene content differences between the HSY and X are greatest in the older stratum, whereas the gene content and order of the collinear regions are identical. Our findings support theoretical models of early sex chromosome evolution

Evolución de los sistemas reproductivos y de los mecanismos de determinación sexual en el género Rumex (Polygonaceae)

Tesis Univ. Granada. Departamento de Genética. Leída el 15 de diciembre de 200