scholarly journals Improving Nelumbo nucifera genome assemblies using high‐resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements

2018 ◽  
Vol 94 (4) ◽  
pp. 721-734 ◽  
Author(s):  
Songtao Gui ◽  
Jing Peng ◽  
Xiaolei Wang ◽  
Zhihua Wu ◽  
Rui Cao ◽  
...  
Keyword(s):  
High Resolution ◽  
Genome Mapping ◽  
Nelumbo Nucifera ◽  
Genetic Maps ◽  
Chromosome Rearrangements ◽  
Genome Assemblies

scholarly journals Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zeratsion Abera Desta ◽  
Bozena Kolano ◽  
Zeeshan Shamim ◽  
Susan J. Armstrong ◽  
Monika Rewers ◽  
...  
Keyword(s):  
Positional Cloning ◽  
Genome Mapping ◽  
Flow Cytometric Analysis ◽  
Genetic Maps ◽  
Cytogenetic Map ◽  
Comparative Maps ◽  
Chromosome Staining ◽  
Genome Assemblies ◽  
Future Work ◽  
Field Cress

AbstractField cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.

scholarly journals High-resolution genetic maps ofLotus japonicusandL. burttiibased on re-sequencing of recombinant inbred lines

DNA Research ◽  
2016 ◽  
Vol 23 (5) ◽  
pp. 487-494 ◽  
Author(s):  
Niraj Shah ◽  
Hideki Hirakawa ◽  
Shohei Kusakabe ◽  
Niels Sandal ◽  
Jens Stougaard ◽  
...  
Keyword(s):  
High Resolution ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Genetic Maps

scholarly journals High Resolution Typing by Whole Genome Mapping Enables Discrimination of LA-MRSA (CC398) Strains and Identification of Transmission Events

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e66493 ◽  
Author(s):  
Thijs Bosch ◽  
Erwin Verkade ◽  
Martijn van Luit ◽  
Bruno Pot ◽  
Paul Vauterin ◽  
...  
Keyword(s):  
High Resolution ◽  
Genome Mapping ◽  
Whole Genome ◽  
Whole Genome Mapping

scholarly journals AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

2020 ◽  
Author(s):  
Kyle Fletcher ◽  
Lin Zhang ◽  
Juliana Gil ◽  
Rongkui Han ◽  
Keri Cavanaugh ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Map ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Whole Genome ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Genome Assemblies

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

scholarly journals A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database

2020 ◽  
Vol 49 (D1) ◽  
pp. D1496-D1501
Author(s):  
Anne V Brown ◽  
Shawn I Conners ◽  
Wei Huang ◽  
Andrew P Wilkey ◽  
David Grant ◽  
...  
Keyword(s):  
Soybean Genome ◽  
Genetic Maps ◽  
Pedigree Information ◽  
Data Sets ◽  
Visualization System ◽  
Interactive Tools ◽  
Genome Viewer ◽  
Reference Quality ◽  
Soybean Genetics ◽  
Genome Assemblies

Abstract SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Gene expression data is presented in the genome viewer as heat maps and pictorial and tabular displays in gene report pages. Millions of sequence variants have been added, representing variations across various collections of cultivars. This variant data is explorable using new interactive tools to visualize the distribution of those variants across the genome, between selected accessions. SoyBase holds several reference-quality soybean genome assemblies, accessible via various query tools and browsers, including a new visualization system for exploring the soybean pan-genome. SoyBase also serves as a nexus of announcements pertinent to the greater soybean research community. The database also includes a soybean-specific anatomic and biochemical trait ontology. The database can be accessed at https://soybase.org.

scholarly journals High-resolution genetic maps ofEucalyptusimproveEucalyptus grandisgenome assembly

2014 ◽  
Vol 206 (4) ◽  
pp. 1283-1296 ◽  
Author(s):  
Jérôme Bartholomé ◽  
Eric Mandrou ◽  
André Mabiala ◽  
Jerry Jenkins ◽  
Ibouniyamine Nabihoudine ◽  
...  
Keyword(s):  
High Resolution ◽  
Genetic Maps

scholarly journals Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Caroline Belser ◽  
Franc-Christophe Baurens ◽  
Benjamin Noel ◽  
Guillaume Martin ◽  
Corinne Cruaud ◽  
...  
Keyword(s):  
Musa Acuminata ◽  
Genetic Maps ◽  
Nanopore Sequencing ◽  
Genome Coverage ◽  
Long Reads ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read ◽  
Genome Assemblies ◽  
First Time

AbstractLong-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes.

Next-generation cytogenomics: High-resolution structural variation detection by optical genome mapping

Cytogenomics ◽  
2021 ◽  
pp. 123-146
Author(s):  
Yannick Delpu ◽  
Hayk Barseghyan ◽  
Sven Bocklandt ◽  
Alex Hastie ◽  
Alka Chaubey
Keyword(s):  
High Resolution ◽  
Structural Variation ◽  
Genome Mapping ◽  
Next Generation

High-resolution FluorescenceIn SituHybridization: A New Approach in Genome Mapping

1996 ◽  
Vol 28 (2) ◽  
pp. 101-106 ◽  
Author(s):  
Aarno Palotie ◽  
Mervi Heiskanen ◽  
Maris Laan ◽  
Nina Horelli-Kuitunen
Keyword(s):  
High Resolution ◽  
Genome Mapping ◽  
New Approach
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