RESUMEN

The common cattle tick Rhipicephalus microplus causes severe limitations to livestock production. Bovine genetics could be a decisive component for the success or failure of control programs for ticks and diseases transmitted. The objective of this work was to detect chromosomal regions associated with host resistance to R. microplus through an associative mapping study using medium and high density microarrays in a population of Argentine Creole cattle. The phenotypic record of the number of ticks that completed their development on the host, after artificial infestations, was obtained during 2015 to 2020. Genomic DNA was extracted for genotyping from 192 animals using Affymetrix high (Axiom™ Bos 1) and medium density (ArBos1) microarrays. In an exploratory study, chromosomal regions containing putative quantitative trait loci (QTLs) were recognized on chromosomes 27, 11, 10, 9, 16, 13, 3, 19, 8 and 18, associated with the variation of R. microplus load. Gene ontology based on genes located on these regions revealed an enrichment of terms and pathways for the immune system, blood coagulation, tissue regeneration, endopeptidase activity and protein phosphorylation. The information obtained in this work constitutes a first report of QTLs for tick count in the Argentine Creole cattle, and contributes with the knowledge about the underlying process involved in tick resistance.

Asunto(s)

Enfermedades de los Bovinos , Sitios de Carácter Cuantitativo , Rhipicephalus , Infestaciones por Garrapatas , Animales , Rhipicephalus/genética , Rhipicephalus/fisiología , Bovinos/genética , Infestaciones por Garrapatas/veterinaria , Infestaciones por Garrapatas/parasitología , Enfermedades de los Bovinos/parasitología , Enfermedades de los Bovinos/genética , Enfermedades de los Bovinos/inmunología , Argentina , Resistencia a la Enfermedad/genética , Femenino , Genotipo , Mapeo Cromosómico/veterinaria

RESUMEN

Over the last 10 years, global raspberry production has increased by 47.89%, based mainly on the red raspberry species (Rubus idaeus). However, the black raspberry (Rubus occidentalis), although less consumed, is resistant to one of the most important diseases for the crop, the late leaf rust caused by Acculeastrum americanum fungus. In this context, genetic resistance is the most sustainable way to control the disease, mainly because there are no registered fungicides for late leaf rust in Brazil. Therefore, the aim was to understand the genetic architecture that controls resistance to late leaf rust in raspberries. For that, we used an interspecific multiparental population using the species mentioned above as parents, 2 different statistical approaches to associate the phenotypes with markers [GWAS (genome-wide association studies) and copula graphical models], and 2 phenotyping methodologies from the first to the 17th day after inoculation (high-throughput phenotyping with a multispectral camera and traditional phenotyping by disease severity scores). Our findings indicate that a locus of higher effect, at position 13.3 Mb on chromosome 5, possibly controls late leaf rust resistance, as both GWAS and the network suggested the same marker. Of the 12 genes flanking its region, 4 were possible receptors, 3 were likely defense executors, 1 gene was likely part of signaling cascades, and 4 were classified as nondefense related. Although the network and GWAS indicated the same higher effect genomic region, the network identified other different candidate regions, potentially complementing the genetic control comprehension.

Asunto(s)

Basidiomycota , Resistencia a la Enfermedad , Estudio de Asociación del Genoma Completo , Fenotipo , Enfermedades de las Plantas , Rubus , Resistencia a la Enfermedad/genética , Rubus/microbiología , Rubus/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Sitios de Carácter Cuantitativo , Hojas de la Planta/microbiología , Hojas de la Planta/genética , Polimorfismo de Nucleótido Simple , Mapeo Cromosómico

RESUMEN

An increase in genetic diversity of bread wheat caused by spring x winter forms leads to an alteration of genetic control of maturity time. Maturity time (MAT) is one of major yield components in wheat, which has two components: the heading date (HD) and grain-filling period (GFP). Using the Illumina Infinium 25k platform we analyzed the genetic control of the HD, GFP and MAT in the F2 and F2:3 populations from a cross between late-ripening spring/winter line 124-1 and spring wheat cultivar Novosibirskaya 31, possessing the same allelic composition of the VRN1 and PPD-D1 genes. The phenotypic evaluation of the populations studied was performed during three years. A total of 17 QTLs were mapped, out of which 4 QTLs for MAT or its components were confirmed over two years. Two common MAT and HD QTLs were identified on the 4A chromosome, and two loci controlling GFP and MAT were found on 6B chromosome. An environmentally stable HD QTL QHd.icg-7B.1 was associated with the FT-B1 gene having a non-synonymous polymorphism [G/C] in its coding region. A novel НD QTL was identified on 7D chromosome. QTL dissection allowed to propose putative genes for QMat.icg4-A and QMat.icg6-B, namely the SPL family gene (TraesCS4A02G359500) and the TCP transcription factor (TraesCS6B02G462100), respectively. The results of this study provide information for further investigation into wheat development.

Asunto(s)

Fenotipo , Sitios de Carácter Cuantitativo , Triticum , Triticum/genética , Triticum/crecimiento & desarrollo , Sitios de Carácter Cuantitativo/genética , Mapeo Cromosómico , Grano Comestible/genética , Factores de Tiempo , Estaciones del Año

RESUMEN

PURPOSE: Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos. METHODS: Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls. RESULTS: Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos. CONCLUSION: Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.

Asunto(s)

Blastocisto , Elementos de Nucleótido Esparcido Largo , Humanos , Elementos de Nucleótido Esparcido Largo/genética , Blastocisto/metabolismo , Femenino , Embrión de Mamíferos/metabolismo , Desarrollo Embrionario/genética , Mutagénesis Insercional/genética , Aneuploidia , Genoma Humano/genética , Fertilización In Vitro , Masculino , Variación Genética/genética , Ratones , Mapeo Cromosómico/métodos

RESUMEN

BACKGROUND: Chronic kidney disease (CKD) is highly prevalent in Central America, and genetic factors may contribute to CKD risk. To understand the influences of genetic admixture on CKD susceptibility, we conducted an admixture mapping screening of CKD traits and risk factors in US Hispanic and Latino individuals from Central America country of origin. METHODS: We analyzed 1023 participants of HCHS/SOL (Hispanic Community Health Study/Study of Latinos) who reported 4 grandparents originating from the same Central America country. Ancestry admixture findings were validated on 8191 African Americans from WHI (Women's Health Initiative), 3141 American Indians from SHS (Strong Heart Study), and over 1.1 million European individuals from a multistudy meta-analysis. RESULTS: We identified 3 novel genomic regions for albuminuria (chromosome 14q24.2), CKD (chromosome 6q25.3), and type 2 diabetes (chromosome 3q22.2). The 14q24.2 locus driven by a Native American ancestry had a protective effect on albuminuria and consisted of 2 nearby regions spanning the RGS6 gene. Variants at this locus were validated in American Indians. The 6q25.3 African ancestry-derived locus, encompassing the ARID1B gene, was associated with increased risk for CKD and replicated in African Americans through admixture mapping. The European ancestry type 2 diabetes locus at 3q22.2, encompassing the EPHB1 and KY genes, was validated in European individuals through variant association. CONCLUSIONS: US Hispanic/Latino populations are culturally and genetically diverse. This study focusing on Central America grandparent country of origin provides new loci discovery and insights into the ancestry-of-origin influences on CKD and risk factors in US Hispanic and Latino individuals.

Asunto(s)

Hispánicos o Latinos , Insuficiencia Renal Crónica , Humanos , Femenino , América Central/etnología , Hispánicos o Latinos/genética , Insuficiencia Renal Crónica/genética , Insuficiencia Renal Crónica/etnología , Masculino , Factores de Riesgo , Persona de Mediana Edad , Albuminuria/genética , Albuminuria/etnología , Anciano , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/epidemiología , Diabetes Mellitus Tipo 2/etnología , Polimorfismo de Nucleótido Simple , Mapeo Cromosómico , Predisposición Genética a la Enfermedad , Adulto , Población Blanca/genética , Negro o Afroamericano/genética

RESUMEN

Potato (Solanum tuberosum) is an essential crop for food security and is ranked as the third most important crop worldwide for human consumption. The Diacol Capiro cultivar holds the dominant position in Colombian cultivation, primarily catering to the food processing industry. This highly heterozygous, autotetraploid cultivar belongs to the Andigenum group and it stands out for its adaptation to a wide variety of environments spanning altitudes from 1,800 to 3,200 meters above sea level. Here, a chromosome-scale assembly, referred to as DC, is presented for this cultivar. The assembly was generated by combining circular consensus sequencing with proximity ligation Hi-C for the scaffolding and represents 2.369 Gb with 48 pseudochromosomes covering 2,091 Gb and an anchor rate of 88.26%. The reference genome metrics, including an N50 of 50.5 Mb, a BUSCO (Benchmarking Universal Single-Copy Orthologue) score of 99.38%, and an Long Terminal Repeat Assembly Index score of 13.53, collectively signal the achieved high assembly quality. A comprehensive annotation yielded a total of 154,114 genes, and the associated BUSCO score of 95.78% for the annotated sequences attests to their completeness. The number of predicted NLR (Nucleotide-Binding and Leucine-Rich-Repeat genes) was 2107 with a large representation of NBARC (for nucleotide binding domain shared by Apaf-1, certain R gene products, and CED-4) containing domains (99.85%). Further comparative analysis of the proposed annotation-based assembly with high-quality known potato genomes, showed a similar genome metrics with differences in total gene numbers related to the ploidy status. The genome assembly and annotation of DC presented in this study represent a valuable asset for comprehending potato genetics. This resource aids in targeted breeding initiatives and contributes to the creation of enhanced, resilient, and more productive potato varieties, particularly beneficial for countries in Latin America.

Asunto(s)

Cromosomas de las Plantas , Genoma de Planta , Anotación de Secuencia Molecular , Solanum tuberosum , Tetraploidía , Solanum tuberosum/genética , Cromosomas de las Plantas/genética , Genómica/métodos , Mapeo Cromosómico

RESUMEN

BACKGROUND: On tropical regions, phosphorus (P) fixation onto aluminum and iron oxides in soil clays restricts P diffusion from the soil to the root surface, limiting crop yields. While increased root surface area favors P uptake under low-P availability, the relationship between the three-dimensional arrangement of the root system and P efficiency remains elusive. Here, we simultaneously assessed allelic effects of loci associated with a variety of root and P efficiency traits, in addition to grain yield under low-P availability, using multi-trait genome-wide association. We also set out to establish the relationship between root architectural traits assessed in hydroponics and in a low-P soil. Our goal was to better understand the influence of root morphology and architecture in sorghum performance under low-P availability. RESULT: In general, the same alleles of associated SNPs increased root and P efficiency traits including grain yield in a low-P soil. We found that sorghum P efficiency relies on pleiotropic loci affecting root traits, which enhance grain yield under low-P availability. Root systems with enhanced surface area stemming from lateral root proliferation mostly up to 40 cm soil depth are important for sorghum adaptation to low-P soils, indicating that differences in root morphology leading to enhanced P uptake occur exactly in the soil layer where P is found at the highest concentration. CONCLUSION: Integrated QTLs detected in different mapping populations now provide a comprehensive molecular genetic framework for P efficiency studies in sorghum. This indicated extensive conservation of P efficiency QTL across populations and emphasized the terminal portion of chromosome 3 as an important region for P efficiency in sorghum. Increases in root surface area via enhancement of lateral root development is a relevant trait for sorghum low-P soil adaptation, impacting the overall architecture of the sorghum root system. In turn, particularly concerning the critical trait for water and nutrient uptake, root surface area, root system development in deeper soil layers does not occur at the expense of shallow rooting, which may be a key reason leading to the distinctive sorghum adaptation to tropical soils with multiple abiotic stresses including low P availability and drought.

Asunto(s)

Estudio de Asociación del Genoma Completo , Fósforo , Raíces de Plantas , Sitios de Carácter Cuantitativo , Sorghum , Sorghum/genética , Sorghum/metabolismo , Sorghum/crecimiento & desarrollo , Fósforo/metabolismo , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/anatomía & histología , Mapeo Cromosómico , Polimorfismo de Nucleótido Simple , Suelo/química , Fenotipo

RESUMEN

BACKGROUND: Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei), such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp. RESULTS: The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The lengths of the male, female, and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. LG18 was found to be the largest for both sexes, whereas LG44 was the shortest for males and LG31 for females. A sex-determining region was found in LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and was able to identify 99% of the males and 88% of the females. Although other significant markers had a lower ability to determine sex, putative genes were intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidates with possible participation in important processes of sexual differentiation in shrimp. CONCLUSIONS: Our results provide novel genomic resources for shrimp, including a high-density linkage map and new insights into the sex-determining region in L. vannamei, which may be usefulfor future genetics and reproduction applications.

Asunto(s)

Mapeo Cromosómico , Penaeidae , Polimorfismo de Nucleótido Simple , Procesos de Determinación del Sexo , Animales , Penaeidae/genética , Femenino , Masculino , Procesos de Determinación del Sexo/genética , Ligamiento Genético , Estudio de Asociación del Genoma Completo

RESUMEN

Physical mapping evidences the chromosome organization and structure. Despite the data about plant cytogenomics, physical mapping has been conducted from single-copy and/or low-copy genes for few species. Carica papaya cytogenomics has been accomplished from BAC-FISH and repeatome sequences. We aimed to map the serk 2, svp-like and mdar 4 sequences in C. papaya. The sequences were amplified and the amplicons sequenced, showing similarity in relation to serk 2, svp-like and mdar 4 genes. Carica papaya diploidy was confirmed and the mitotic chromosomes characterized. The chromosome 1 exhibited the secondary constriction pericentromeric to the centromere of the long arm. So, we concluded that it is the sex chromosomes. serk 2 was mapped in the long arm interstitial portion of the sex chromosomes, and the interphase nuclei showed two fluorescence signals. Considering these results and the sequencing data from the C. papaya sex chromosomes, svp-like and mdar 4 genes were mapped in the interstitial region of the sex chromosome long arm. Both sequences showed only one fluorescence signal in the interphase nuclei. The procedure adopted here can be reproduced for other single-copy and/or low-copy genes, allowing the construction of cytogenetic maps. In addition, we revisited the cytogenomics data about C. papaya sex chromosomes, presenting a revised point of view about the structure and evolution to these chromosomes.

Asunto(s)

Carica , Cromosomas de las Plantas , Cromosomas Sexuales , Carica/genética , Cromosomas de las Plantas/genética , Cromosomas Sexuales/genética , Mapeo Físico de Cromosoma , Hibridación Fluorescente in Situ/métodos , Proteínas de Plantas/genética , Mapeo Cromosómico , Genes de Plantas

RESUMEN

Ctenoluciidae is a Neotropical freshwater fish family composed of two genera, Ctenolucius (C. beani and C. hujeta) and Boulengerella (B. cuvieri, B. lateristriga, B. lucius, B. maculata, and B. xyrekes), which present diploid number conservation of 36 chromosomes and a strong association of telomeric sequences with ribosomal DNAs. In the present study, we performed chromosomal mapping of microsatellites and transposable elements (TEs) in Boulengerella species and Ctenolucius hujeta. We aim to understand how those sequences are distributed in these organisms' genomes and their influence on the chromosomal evolution of the group. Our results indicate that repetitive sequences may had an active role in the karyotypic diversification of this family, especially in the formation of chromosomal hotspots that are traceable in the diversification processes of Ctenoluciidae karyotypes. We demonstrate that (GATA)n sequences also accumulate in the secondary constriction formed by the 18 S rDNA site, which shows consistent size heteromorphism between males and females in all Boulengerella species, suggesting an initial process of sex chromosome differentiation.

Asunto(s)

Characiformes , Mapeo Cromosómico , Secuencias Repetitivas de Ácidos Nucleicos , Retroelementos , Animales , Characiformes/genética , Masculino , Femenino , Retroelementos/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Evolución Molecular , Repeticiones de Microsatélite/genética , Cariotipo , Cromosomas/genética

RESUMEN

Avian genomes are characterized as being more compact than other amniotes, with less diversity and density of transposable elements (TEs). In addition, birds usually show bimodal karyotypes, exhibiting a great variation in diploid numbers. Some species present unusually large sex chromosomes, possibly due to the accumulation of repetitive sequences. Avian retrotransposon-like element (AviRTE) is a long interspersed nuclear element (LINE) recently discovered in the genomes of birds and nematodes, and it is still poorly characterized in terms of chromosomal mapping and phylogenetic relationships. In this study, we mapped AviRTE isolated from the Trogon surrucura genome into the T. surrucura (TSU) karyotype. Furthermore, we analyzed the phylogenetic relationships of this LINE in birds and other vertebrates. Our results showed that the distribution pattern of AviRTE is not restricted to heterochromatic regions, with accumulation on the W chromosome of TSU, yet another species with an atypical sex chromosome and TE hybridization. The phylogenetic analysis of AviRTE sequences in birds agreed with the proposed phylogeny of species in most clades, and allowed the detection of this sequence in other species, expanding the distribution of the element.

Asunto(s)

Aves , Mapeo Cromosómico , Cariotipo , Filogenia , Retroelementos , Cromosomas Sexuales , Animales , Aves/genética , Aves/clasificación , Cromosomas Sexuales/genética , Masculino , Femenino , Elementos de Nucleótido Esparcido Largo

RESUMEN

INTRODUCTION: Currently, there are 38 valid species of freshwater stingrays, and these belong to the subfamily Potamotrygoninae. However, cytogenetic information about this group is limited, with studies mainly using classical techniques, Giemsa, and C-banding. METHODS: In this study, we used classical and molecular cytogenetic techniques - mapping of 18S and 5S rDNA and simple sequence repeats (SSRs) - in order to investigate the karyotypic composition of Potamotrygon schroederi and reveal the karyoevolutionary trends of this group. RESULTS: The species presented 2n = 66 chromosomes with 18m + 12sm + 16st + 20a, heterochromatic blocks distributed in the centromeric regions of all the chromosomes, and terminal blocks in the q arm of pairs 2 and 3. Mapping of 18S rDNA regions revealed multiple clusters on pairs 2 and 7 and a homolog of pair 24. The 5S rDNA region was found in the pericentromeric portion of the subtelocentric pair 16. Furthermore, dinucleotide SSRs sequences were found in the centromeric and terminal regions of different chromosomal pairs, with preferential accumulation in pair 17. In addition, we identified conspicuous blocks of (GATA)n and (GACA)n sequences colocalized with the 5S rDNA (pair 16). CONCLUSION: In general, this study corroborates the general trend of a reduction in 2n in the species of Potamotrygoninae subfamily. Moreover, we found that the location of rDNA regions is very similar among Potamotrygon species, and the SSRs accumulation in the second subtelocentric pair (17) seems to be a common trait in this genus.

Asunto(s)

Cariotipo , Animales , ARN Ribosómico 5S/genética , Repeticiones de Microsatélite/genética , ARN Ribosómico 18S/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , ADN Ribosómico/genética , Centrómero/genética , Cariotipificación , Hibridación Fluorescente in Situ , Mapeo Cromosómico , Bandeo Cromosómico

RESUMEN

The species Passiflora alata, P. cincinnata, and P. edulis have great economic value due to the use of their fruits for human consumption. In this study, we compared the repetitive genome fractions of these three species. The compositions of the repetitive DNA of these three species' genomes were analyzed using clustering and identification of the repetitive sequences with RepeatExplorer. It was found that repetitive DNA content represents 74.70%, 66.86%, and 62.24% of the genome of P. alata, P. edulis, and P. cincinnata, respectively. LTR Ty3/Gypsy retrotransposons represent the highest genome proportions in P. alata and P. edulis, while Ty1/Copia comprises the largest proportion of P. cincinnata genome. Chromosomal mapping by Fluorescent In Situ Hybridization (FISH) showed that LTR retrotransposons have a dispersed distribution along chromosomes. The subtelomeric region of chromosomes is where 145 bp satellite DNA is located, suggesting that these elements may play important roles in genome structure and organization in these species. In this work, we obtained the first global characterization of the composition of repetitive DNA in Passiflora, showing that an increase in genome size is related to an increase in repetitive DNA, which represents an important evolutionary route for these species.

Asunto(s)

ADN Satélite , Genoma de Planta , Passiflora , Retroelementos , Passiflora/genética , ADN Satélite/genética , Retroelementos/genética , Cromosomas de las Plantas/genética , Elementos Transponibles de ADN/genética , ADN de Plantas/genética , Hibridación Fluorescente in Situ , Mapeo Cromosómico

RESUMEN

Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun., using PacBio long-read sequencing, optical mapping, and Hi-C scaffolding technologies. The final sequence assembly consisted of 737.9 Mb, among which 647.0 Mb were anchored to the 12 chromosomes. Compared with chromosome-scale assemblies of S. lycopersicum (tomato), S. etuberosum (non-tuber-bearing species with E-genome), S. verrucosum, S. chacoense, S. multidissectum, and S. phureja (all four are A-genome species), the S. bulbocastnum genome was the shortest. It contained fewer transposable elements (56.2%) than A-genome species. A cluster analysis was performed based on pairwise ratios of syntenic regions among the seven chromosome-scale assemblies, showing that the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum. Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species. Therefore, the S. bulbocastanum genome differs in genome structure and gene sequences from the A-genome species. These findings provide important insights into understanding and utilizing the genetic diversity of S. bulbocastanum and the other Mexican diploid species in potato breeding.

Asunto(s)

Diploidia , Genoma de Planta , Solanum , Solanum/genética , Solanum tuberosum/genética , Cromosomas de las Plantas/genética , Anotación de Secuencia Molecular , Genómica/métodos , Mapeo Cromosómico , Filogenia , México

RESUMEN

Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries-one from a female and another from a male-with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further research.

Asunto(s)

Peces Planos , Lenguado , Animales , Masculino , Femenino , Lenguado/genética , Peces Planos/genética , Tamaño del Genoma , Mapeo Cromosómico , Genómica

RESUMEN

Cytogenetics has allowed the investigation of chromosomal diversity and repetitive genomic content in wasps. In this study, we characterized the karyotype of the social wasp Mischocyttarus cassununga using conventional cytogenetics and chromosomal mapping of repetitive sequences. This study was undertaken to extend our understanding of the genomic organization of repetitive DNA in social wasps and is the first molecular cytogenetic insight into the genus Mischocyttarus. The karyotype of M. cassununga had a chromosome number of 2n = 64 for females and n = 32 for males. Constitutive heterochromatin exhibited three distribution patterns: centromeric and pericentromeric regions along the smaller arms and extending almost the entire chromosome. The major ribosomal DNA sites were located on chromosome pair in females and one chromosome in males. Positive signals for the microsatellite probes (GA)n and (GAG)n were observed in the euchromatic regions of all chromosomes. The microsatellites, (CGG)n, (TAT)n, (TTAGG)n, and (TCAGG)n were not observed in any region of the chromosomes. Our results contrast with those previously obtained for Polybia fastidiosuscula, which showed that the microsatellites (GAG)n, (CGG)n, (TAT)n, (TTAGG)n, and (TCAGG)n are located predominantly in constitutive heterochromatin. This suggests variations in the diversity and chromosomal organization of repetitive sequences in the genomes of social wasps.

Asunto(s)

Heterocromatina , Repeticiones de Microsatélite , Avispas , Animales , Avispas/genética , Femenino , Masculino , Heterocromatina/genética , Cromosomas de Insectos/genética , Mapeo Cromosómico , Cariotipo , Hibridación Fluorescente in Situ , Análisis Citogenético

RESUMEN

Globally, millions of lives are impacted every year by infectious diseases outbreaks. Comprehensive and innovative surveillance strategies aiming at early alert and timely containment of emerging and reemerging pathogens are a pressing priority. Shortcomings and delays in current pathogen surveillance practices further disturbed informing responses, interventions, and mitigation of recent pandemics, including H1N1 influenza and SARS-CoV-2. We present the design principles of the architecture for an early-alert surveillance system that leverages the vast available data landscape, including syndromic data from primary health care, drug sales, and rumors from the lay media and social media to identify areas with an increased number of cases of respiratory disease. In these potentially affected areas, an intensive and fast sample collection and advanced high-throughput genome sequencing analyses would inform on circulating known or novel pathogens by metagenomics-enabled pathogen characterization. Concurrently, the integration of bioclimatic and socioeconomic data, as well as transportation and mobility network data, into a data analytics platform, coupled with advanced mathematical modeling using artificial intelligence or machine learning, will enable more accurate estimation of outbreak spread risk. Such an approach aims to readily identify and characterize regions in the early stages of an outbreak development, as well as model risk and patterns of spread, informing targeted mitigation and control measures. A fully operational system must integrate diverse and robust data streams to translate data into actionable intelligence and actions, ultimately paving the way toward constructing next-generation surveillance systems.

Asunto(s)

Inteligencia Artificial , Subtipo H1N1 del Virus de la Influenza A , Humanos , Subtipo H1N1 del Virus de la Influenza A/genética , Mapeo Cromosómico , Ciencia de los Datos , Brotes de Enfermedades/prevención & control

RESUMEN

Among Bemisia tabaci species, the invasive MEAM1 and MED species are key agricultural pests for many crops. In Brazil, most part of B. tabaci population outbreaks were associated with MEAM1, which, since 1990s quickly spread across the entire country. Later in 2014, the MED was identified in Brazil, initially more restricted to greenhouses, but suddenly reaching new areas in the South and Southeast open regions. Thus, our objective was to investigate the geographical distribution of MEAM1 and MED on open field crops in Brazil. MEAM1 is still the predominant species on open field crops such as soybean, cotton, and tomato. The sequencing of a cytochrome c oxidase subunit I (COI) gene fragment revealed a single haplotype of MEAM1, suggesting the establishment of a single MEAM1 strain in the country. The haplotypes found for MEAM1 and MED are genetically related to the globally dispersed strains, Jap1 and Mch1, respectively. Continuous monitoring of B. tabaci species is crucial because landscape alterations, climatic changes, and pest management methods may shift the B. tabaci species distribution and dominance in Brazilian crop areas.

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Dentre as espécies de Bemisia tabaci, as espécies invasoras MEAM1 e MED se destacam como pragas de grande importância para várias culturas. No Brasil, a maior parte dos surtos populacionais de mosca-branca são associados a presença da espécie MEAM1, que a partir 1990 se espalhou por todo o país. Por outro lado, em 2014 a espécie MED foi identificada no Brasil, inicialmente restrita a casas de vegetação, mas rapidamente se difundindo em novas áreas nas regiões Sul e Sudeste do Brasil. Assim, nosso objetivo foi investigar a distribuição geográfica das espécies MEAM1 e MED em grandes culturas no Brasil. A espécie MEAM1 continua sendo predominante nas monoculturas como algodão, soja e tomate. O sequenciamento de um fragmento do gene citocromo c oxidase subunidade I (COI) revelou a presença de um haplótipo para MEAM1, sugerindo o estabelecimento de apenas uma linhagem no país. Os haplótipos encontrados para MEAM1 e MED são geneticamente relacionados as linhagens globalmente dispersas Jap1 e Mch1, respectivamente. O monitoramento contínuo das espécies de B. tabaci é crucial pois as mudanças na paisagem, mudanças climáticas e métodos de manejo das pragas podem alterar a dominância e a distribuição dessas espécies nas áreas agrícolas do Brasil.

Asunto(s)

Animales , Control de Plagas , Mapeo Cromosómico , Plagas Agrícolas

RESUMEN

Anthracnose (ANT) and angular leaf spot (ALS) are significant diseases in common bean, leading to considerable yield losses under specific environmental conditions. The California Dark Red Kidney (CDRK) bean cultivar is known for its resistance to multiple races of both pathogens. Previous studies have identified the CoPv01CDRK/PhgPv01CDRK resistance loci on chromosome Pv01. Here, we evaluated the expression levels of ten candidate genes near the CoPv01CDRK/PhgPv01CDRK loci and plant defense genes using quantitative real-time PCR in CDRK cultivar inoculated with races 73 of Colletotrichum lindemuthianum and 63-39 of Pseudocercospora griseola. Gene expression analysis revealed that the Phvul.001G246300 gene exhibited the most elevated levels, showing remarkable 7.8-fold and 8.5-fold increases for ANT and ALS, respectively. The Phvul.001G246300 gene encodes an abscisic acid (ABA) receptor with pyrabactin resistance, PYR1-like (PYL) protein, which plays a central role in the crosstalk between ABA and jasmonic acid responses. Interestingly, our results also showed that the other defense genes were initially activated. These findings provide critical insights into the molecular mechanisms underlying plant defense against these diseases and could contribute to the development of more effective disease management strategies in the future.

Asunto(s)

Colletotrichum , Phaseolus , Mapeo Cromosómico , Colletotrichum/genética , Resistencia a la Enfermedad/genética , Ligamiento Genético , Marcadores Genéticos , Riñón , Phaseolus/genética , Enfermedades de las Plantas/genética

RESUMEN

In the Amazon, some species of Loricariidae are at risk of extinction due to habitat loss and overexploitation by the ornamental fish market. Cytogenetic data related to the karyotype and meiotic cycle can contribute to understanding the reproductive biology and help management and conservation programs of these fish. Additionally, chromosomal mapping of repetitive DNA in Loricariidae may aid comparative genomic studies in this family. However, cytogenetics analysis is limited in Amazonian locariids. In this study, chromosomal mapping of multigenic families was performed in Scobinancistrus aureatus, Scobinancistrus pariolispos and Spatuloricaria sp. Meiotic analyzes were performed in Hypancistrus zebra and Hypancistrus sp. "pão". Results showed new karyotype for Spatuloricaria sp. (2n=66, NF=82, 50m-10sm-6m). Distinct patterns of chromosomal organization of histone H1, histone H3 and snDNA U2 genes were registered in the karyotypes of the studied species, proving to be an excellent cytotaxonomic tool. Hypotheses to explain the evolutionary dynamics of these sequences in studied Loricariidae were proposed. Regarding H. zebra and H. sp. "pão", we describe the events related to synapse and transcriptional activity during the meiotic cycle, which in both species showed 26 fully synapsed bivalents, with high gene expression only during zygotene and pachytene. Both Hypancistrus species could be used may be models for evaluating changes in spermatogenesis of Loricariidae.

Asunto(s)

Bagres , Animales , Masculino , Bagres/genética , Brasil , Familia de Multigenes , Mapeo Cromosómico , Cariotipo