Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection

2022 ◽  
pp. 245-257
Author(s):  
Yuxuan Yuan
Keyword(s):  
Genome Assembly ◽  
Structural Variation ◽  
Optical Mapping ◽  
Plant Genome

scholarly journals Single-molecule analysis reveals widespread structural variation in multiple myeloma

2015 ◽  
Vol 112 (25) ◽  
pp. 7689-7694 ◽  
Author(s):  
Aditya Gupta ◽  
Michael Place ◽  
Steven Goldstein ◽  
Deepayan Sarkar ◽  
Shiguo Zhou ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Tumor Progression ◽  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Plasma Cells ◽  
Optical Mapping ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Whole Genome Analysis

Multiple myeloma (MM), a malignancy of plasma cells, is characterized by widespread genomic heterogeneity and, consequently, differences in disease progression and drug response. Although recent large-scale sequencing studies have greatly improved our understanding of MM genomes, our knowledge about genomic structural variation in MM is attenuated due to the limitations of commonly used sequencing approaches. In this study, we present the application of optical mapping, a single-molecule, whole-genome analysis system, to discover new structural variants in a primary MM genome. Through our analysis, we have identified and characterized widespread structural variation in this tumor genome. Additionally, we describe our efforts toward comprehensive characterization of genome structure and variation by integrating our findings from optical mapping with those from DNA sequencing-based genomic analysis. Finally, by studying this MM genome at two time points during tumor progression, we have demonstrated an increase in mutational burden with tumor progression at all length scales of variation.

scholarly journals A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

2020 ◽  
Author(s):  
Kumar Paritosh ◽  
Akshay Kumar Pradhan ◽  
Deepak Pental
Keyword(s):  
Genome Assembly ◽  
Optical Mapping ◽  
Indian Subcontinent ◽  
Brassica Nigra ◽  
Oilseed Crop ◽  
B Genome ◽  
Oxford Nanopore ◽  
Long Read ◽  
Black Mustard ◽  
Genome Assemblies

AbstractBrassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B. juncea (AABB), an important oilseed crop of the Indian subcontinent. We report here a highly contiguous genome assembly of B. nigra variety Sangam. The genome assembly has been carried out using Oxford Nanopore long-read sequencing and optical mapping. The resulting chromosome-scale assembly is a significant improvement over the previous draft assemblies of B. nigra; five out of the eight pseudochromosomes were represented by one scaffold each. The assembled genome was annotated for the transposons, centromeric repeats, and genes. The B. nigra genome was compared with the recently available contiguous genome assemblies of B. rapa (AA), B. oleracea (CC), and B. juncea (AABB). Based on the maximum homology among the three diploid genomes of U’s triangle, we propose a new nomenclature for B. nigra pseudochromosomes, taking the B. rapa pseudochromosome nomenclature as the reference.

scholarly journals A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps

2021 ◽  
Author(s):  
Natalya Kudryavtseva ◽  
Aleksey Ermolaev ◽  
Gennady Karlov ◽  
Ilya Kirov ◽  
Masayoshi Shigyo ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Assembly ◽  
Genetic Maps ◽  
Plant Genome ◽  
Probe Design ◽  
Fish Technique ◽  
Plant Chromosomes ◽  
Dual Color ◽  
Chromosome Level

In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refin-ing of genetic maps and validation genome assembly at the chromosomal level. Despite tremen-dous progress in genome sequencing the plant genome assembly at chromosome level still remain a challenge. Recently developed optical and Hi-C mapping aim to assist in genome assembly. For high-confidence in the genome assembly at chromosome level more independent approaches will be required. The present study aimed to refined an ultrasensitive Tyr-FISH technique and to de-velop a reliable and easy method for in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH technique to find out the reasons for the failures of using the method. It has been shown that successful visualization of marker/gene depends significantly on method of chromosome slide preparation, probe design and labelling, high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.7Kb with a frequency of 51.6%. Based on our results, we developed a reliable and simple protocol for dual-color Tyr-FISH visualization of short unique DNA sequences on plant chromosomes. New protocol allows more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps.

scholarly journals Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2681
Author(s):  
Ilya Kirov ◽  
Pavel Merkulov ◽  
Maxim Dudnikov ◽  
Ekaterina Polkhovskaya ◽  
Roman A. Komakhin ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Assembly ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Gag Protein ◽  
Reading Frame ◽  
Retrotransposon Family ◽  
Long Read ◽  
Low Coverage ◽  
Arabidopsis Thaliana Genome

Long-read data is a great tool to discover new active transposable elements (TEs). However, no ready-to-use tools were available to gather this information from low coverage ONT datasets. Here, we developed a novel pipeline, nanotei, that allows detection of TE-contained structural variants, including individual TE transpositions. We exploited this pipeline to identify TE insertion in the Arabidopsis thaliana genome. Using nanotei, we identified tens of TE copies, including ones for the well-characterized ONSEN retrotransposon family that were hidden in genome assembly gaps. The results demonstrate that some TEs are inaccessible for analysis with the current A. thaliana (TAIR10.1) genome assembly. We further explored the mobilome of the ddm1 mutant with elevated TE activity. Nanotei captured all TEs previously known to be active in ddm1 and also identified transposition of non-autonomous TEs. Of them, one non-autonomous TE derived from (AT5TE33540) belongs to TR-GAG retrotransposons with a single open reading frame (ORF) encoding the GAG protein. These results provide the first direct evidence that TR-GAGs and other non-autonomous LTR retrotransposons can transpose in the plant genome, albeit in the absence of most of the encoded proteins. In summary, nanotei is a useful tool to detect active TEs and their insertions in plant genomes using low-coverage data from Nanopore genome sequencing.

scholarly journals Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping

2018 ◽  
Vol 9 ◽  
Author(s):  
Yuxuan Yuan ◽  
Zbyněk Milec ◽  
Philipp E. Bayer ◽  
Jan Vrána ◽  
Jaroslav Doležel ◽  
...  
Keyword(s):  
Large Scale ◽  
Structural Variation ◽  
Optical Mapping ◽  
Subterranean Clover

scholarly journals De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

2015 ◽  
Vol 8 (3) ◽  
pp. 489-492 ◽  
Author(s):  
Ting Xie ◽  
Jue-Fei Zheng ◽  
Sheng Liu ◽  
Cheng Peng ◽  
Yong-Ming Zhou ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Assembly ◽  
De Novo ◽  
Plant Genome ◽  
Chromatin Interactions

scholarly journals Optical Mapping of the Fusarium oxysporum f. sp. melongenae Genome

2021 ◽  
Author(s):  
Duygu Ates ◽  
Hacer Handan Altinok ◽  
Bahattin Tanyolaç
Keyword(s):  
Fusarium Oxysporum ◽  
Genome Assembly ◽  
High Efficiency ◽  
Reference Genome ◽  
Optical Mapping ◽  
Low Cost ◽  
Accession Number ◽  
Optical Map ◽  
Genomic Studies

Abstract Optical mapping approaches are widely preferred and applied in different branches of genomic studies because of their accuracy, low cost, and high efficiency. In the current study, a sequence orientation of the Fusarium oxysporum f. sp. melongenae (FOMG) genome that is deposited in GenBank NCBI under accession number MPIL00000000 was used as the reference genome, which we checked with Bionano Genomics (BNG) optical mapping approaches. BNG optical mapping produced 103 contigs, the longest of which was 3.05 Mb. The N50 value of BNG contigs is 0.85 Mb. The sequences of the FOMG reference genome and BNG optical map mainly match each other. Results obtained in the current study indicate that BNG optical mapping can be used to construct complete and gapless assemblies of the FOMG genome. It also can be applied to validate a previous genome assembly.

scholarly journals OptiDiff: structural variation detection from single optical mapping reads

2022 ◽  
Author(s):  
Mehmet Akdel ◽  
Dick de Ridder
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Optical Mapping ◽  
Cost Effective ◽  
Sequencing Data ◽  
Mapping Technology ◽  
Cost Effective Alternative ◽  
Algorithmic Approaches ◽  
Broad Interest

Detecting structural variation (SV) in eukaryotic genomes is of broad interest due to its often dramatic phenotypic effects, but remains a major, costly challenge based on DNA sequencing data. A cost-effective alternative in detecting large-scale SV has become available with advances in optical mapping technology. However, the algorithmic approaches to identifying SVs from optical mapping data are limited. Here, we propose a novel, open-source SV detection tool, OptiDiff, which employs a single molecule based approach to detect and classify homozygous and heterozygous SVs at coverages as low as 20x, showing better performance than the state of the art.

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