Karyotype differentiation in cultivated chickpea revealed by Oligopainting fluorescence in situ hybridization

Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of the chickpea genome at the chromosomal level, including the long-range molecular chromosome organization, is limited. Earlier cytogenetic studies in chickpea suffered from a limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-fluorescence in situ hybridization (FISH) barcodes for the identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes. Thus, oligo-FISH appears as a powerful tool not only for comparative karyotyping but also for the validation of genome assemblies

Geostatistical and geospatial assessment of soil pollution with heavy metals in Pavlograd city (Ukraine)

This paper presents the result of studies of the geostatistical and geospatial assessment heavy metal pollution in soils caused by various technogenic sources to assess the environmental impact of industrial agglomeration activitiy in the Pavlograd city. The main sources of technogenic pollution in the Pavlograd city and suburban areas are industrial enterprises, coal-fired plants, mine dumps and other. The vast number of analyzed soil samples with weakly acidic pH values from 6.3 to 6.8 is characterized as loam (63 %), the rest are sand (33 %) and clay soils (4 %). The correlation matrix of metals data indicates positive correlation with correlation coefficient r 2 > 0.5 among texture – Ni (0.705) and Pb – Zn (0.695) within the Pavlograd city area. In the case of Cu (2.73) and Cd (4.27), the geoaccumulation index indicated “moderately to strongly” and “strongly to extremely” polluted soils accordingly. Means of pollution index (PI) for heavy metals were between uncontaminated ( PI ≤ 1) and of moderate contaminated soils ( PI ≥ 1).The results of this study show that industrial enterprises’ activities lead to heavy metal contamination in the topsoil of the studied sites and close to the background values. Similar properties were confirmed by principal component analysis (PCA) and cluster analysis. The PCA and cluster analysis results indicate that Cd, Ni, Pb, Cu, Zn and Mn in topsoil were affected by the technogenic activity. The spatial distribution characteristics of Cu, Pb, Cd and Zn in the geochemical maps are also similar. Highlighted are some of the halos in Pavlograd of high density of total soil contamination with heavy metals. The metals come from anthropogenic sources, mainly produced with four industrial enterprises in Pavlograd city. Mostly they are concentrated in the Southeast and West of the city and suburban areas of the Pavlograd district. Therefore, it is necessary arrangements to predict of the development of ecologically dangerous state of environmental pollution within the area of industrial enterprises of city

Research gaps and challenges in the conservation and use of North American wild lettuce germplasm

The North American crop wild relatives (CWR) of lettuce (Lactuca L.) represent an underexplored pool of genetic diversity of potential value to breeding programs. The 10 species belong to three different groups: a native clade including at least six allotetraploid species [L. biennis (Moench) Fernald, L. canadensis L., L. floridana (L.) Gaertn., L. graminifolia Michx., L. hirsuta Muhl. ex Nutt., and L. ludoviciana (Nutt.) Riddell], a diploid clade with one species [L. tatarica (L.) C. A. Mey. subsp. pulchella (Pursh) Stebbins], and a clade related to the cultivated taxon (L. sativa L.) with three non‐native species (L. saligna L., L. serriola L., and L. virosa L.). In this review, we examine the role of herbarium and genebank holdings in taxonomic and other foundational studies, as well as for germplasm exploration and use. We compile the state of knowledge on the ranges of lettuce CWR in North America, modeling the potential distributions of the species and assessing their ex situ and (for native species) in situ conservation status. We categorize seven of the species as high priority for further conservation and three as medium priority, with none currently considered low priority or sufficiently conserved. Further, we review morphological, phenological, genetic diversity, and pest and disease information with regard to North American species. We conclude by outlining the critical gaps and describing a way forward for addressing challenges in the conservation and use of North American wild lettuce germplasm

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Wild Lactuca Species in North America

This chapter presents a brief history of the uses of lettuce (Lactuca sativa L.) and its wild North American relatives, and reviews the agricultural importance of lettuce and challenges in its cultivation, in relation to nutritional quality, diseases, pests, and edaphic and climatic limitations. The evolution and taxonomy of the genus Lactuca are presented, with a primary focus on the wild Lactuca species of North America, their characterization, biogeography and distribution, habitat ecology, and genepools. Specific examples of phenotypic variability, genetic diversity and disease resistance of wild Lactuca taxa from both published reports and recent evaluations conducted in our laboratory are also presented. The past (and future) exploitation of wild Lactuca relatives in lettuce breeding is examined and discussed in the broader context of crop improvement. The current status of in situ and ex situ conservation of wild and weedy North American Lactuca is reviewed, along with recommendations on how these genetic resources could be better conserved and utilized.This is a manuscript of a chapter published as Lebeda A., Křístková E., Doležalová I., Kitner M., Widrlechner M.P. (2019) Wild Lactuca Species in North America. In: Greene S., Williams K., Khoury C., Kantar M., Marek L. (eds) North American Crop Wild Relatives, Volume 2. Springer, Cham. doi: 10.1007/978-3-319-97121-6_5. Posted with permission.</p