Genome Mapping in Plant Comparative Genomics

Chaney, Lindsay; Sharp, Aaron R.; Evans, Carrie R.; Udall, Joshua A.

doi:10.1016/j.tplants.2016.05.004

Cited by 35 publications

(25 citation statements)

References 82 publications

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“…The characteristics and features of Bionano technology have been reviewed elsewhere (Levy-Sakin and Ebenstein, 2013;Tang et al, 2015;Chaney et al, 2016;Yuan et al, 2017). Briefly, the method involves purifying high molecular weight (HMW) DNA and treating with a nickase, a modified restriction enzyme that creates single stranded nicks.…”

Section: Validation Of Sequence Assemblymentioning

confidence: 99%

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Udall

Dawe

2017

Plant Cell

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ORCID ID: 0000-0003-0978-4764 (J.A.U.)Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.

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Section: Validation Of Sequence Assemblymentioning

confidence: 99%

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Udall

Dawe

2017

Plant Cell

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“…Once complete, reference genomes become valuable tools for studying structural variation, DNA rearrangements, association genetics, and polyploid genome evolution . Reference genomes, including non‐coding regions, are essential for bridging genomics to weed management by enabling studies to understand evolution, domestication, phylogeny, reproduction, invasiveness, and herbicide resistance in weedy species.…”

Section: The State Of the Art In Genomics And Weed Genomicsmentioning

confidence: 99%

“…24,25 Once complete, reference genomes become valuable tools for studying structural variation, DNA rearrangements, association genetics, and polyploid genome evolution. 26 Reference genomes, including non-coding regions, are essential for bridging genomics to weed management by enabling studies to understand evolution, domestication, phylogeny, reproduction, invasiveness, and herbicide resistance in weedy species. In short, technological advancements have drastically enabled genome reconstruction efforts to deliver more complete, contiguous, and accurate genome assemblies for more complex species, which is necessary to deliver on the promise of weed genomics to improve weed management.…”

Section: Introductionmentioning

confidence: 99%

The power and potential of genomics in weed biology and management

Ravet

Patterson

Krähmer

et al. 2018

Pest Management Science

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There have been previous calls for, and efforts focused on, realizing the power and potential of weed genomics for better understanding of weeds. Sustained advances in genome sequencing and assembly technologies now make it possible for individual research groups to generate reference genomes for multiple weed species at reasonable costs. Here, we present the outcomes from several meetings, discussions, and workshops focused on establishing an International Weed Genomics Consortium (IWGC) for a coordinated international effort in weed genomics. We review the 'state of the art' in genomics and weed genomics, including technologies, applications, and on-going weed genome projects. We also report the outcomes from a workshop and a global survey of the weed science community to identify priority species, key biological questions, and weed management applications that can be addressed through greater availability of, and access to, genomic resources. Major focus areas include the evolution of herbicide resistance and weedy traits, the development of molecular diagnostics, and the identification of novel targets and approaches for weed management. There is increasing interest in, and need for, weed genomics, and the establishment of the IWGC will provide the necessary global platform for communication and coordination of weed genomics research. © 2018 Society of Chemical Industry.

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“…Optical mapping is an approach that combines DNA tagging with imaging to produce an ordered map of restriction sites or sequence motifs from a single linearized DNA molecule (Chaney et al, 2016). There are two commercial vendors with slightly different variation of conceptually similar technologies -OpGen and BioNano (Tang et al, 2015).…”

Section: Optical Mappingmentioning

confidence: 99%

“…Although so far very few studies plant structural variations were studied using optical mapping, there have been emerging proposals and pilot studies to map many individuals using optical mapping related technologies (Chaney et al, 2016).…”

Section: Optical Mappingmentioning

confidence: 99%

Cataloging Plant Genome Structural Variations

Zhang¹,

Liang²,

Tang³

2018

Current Issues in Molecular Biology

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Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next-generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the 'hidden' diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs. Specific examples are chosen to demonstrate the genetic basis for phenotype diversity in model plant and major agricultural crops. Additionally, development of new genomic mapping technologies, including optical mapping and long read sequencing, as well as improved computational algorithms associated with these technologies have helped to pinpoint the exact nature and location of genomic SVs with much better resolution and precision. Future direction of plant research on SVs should focus on the population level to build a comprehensive catalogue of SVs, leading to full assessment of their impact on biological diversity.

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Genome Mapping in Plant Comparative Genomics

Cited by 35 publications

References 82 publications

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

The power and potential of genomics in weed biology and management

Cataloging Plant Genome Structural Variations

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