Assembly and Phasing of Complex Genomes in Plant

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 3130

Special Issue Editors


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Guest Editor
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 311300, China
Interests: bioinformatics; genomics; plant breeding

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Guest Editor
College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
Interests: bioinformatics; plant genomics; evolution
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Guest Editor
Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
Interests: genomics, transcriptomics and plant breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The journal Plants is going to publish a Special Issue of “Assembly and phasing of complex genomes in Plant”. Most genome sequencing projects have released mosaic assemblies with a mix of alleles from different parents. Nevertheless, genomes of organisms are phased in the nucleus, and traditional assembly strategies fail to take into account allelic variation, which is crucial and leads to phenotypic outcomes. Plant genome studies have shown the importance of haplotype-resolved genome assembly for tackling complex biological questions including mechanisms of genome evolution, heterosis, and phenotypic variation. We intend to cover a wide range of haplotype-resolved genome assemblies in this special issue. This special issue will also highlight new technologies or methods in this area.

Prof. Dr. Xingtan Zhang
Prof. Dr. Xuepeng Sun
Prof. Dr. Won C. Yim
Guest Editors

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Keywords

  • haplotype-resolved genome assembly
  • haplotype phasing
  • allelic variation
  • heterozygous diploid genome
  • polyploid gnome

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Published Papers (1 paper)

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Research

12 pages, 1772 KiB  
Article
Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions
by Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato and Massimo Delledonne
Plants 2023, 12(2), 320; https://doi.org/10.3390/plants12020320 - 10 Jan 2023
Viewed by 2409
Abstract
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the [...] Read more.
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the structural solidity of Hi-C reconstructed scaffolds. Optical maps were used to assess the correctness of five de novo genome assemblies based on long-read sequencing for contig generation and Hi-C for scaffolding. Hundreds of inconsistencies were found between the reconstructions generated using the Hi-C and optical mapping approaches. Manual inspection, exploiting raw long-read sequencing data and optical maps, confirmed that several of these conflicts were derived from Hi-C joining errors. Such misjoins were widespread, involved the connection of both small and large contigs, and even overlapped annotated genes. We conclude that the integration of optical mapping data after, not before, Hi-C-based scaffolding, improves the quality of the assembly and limits reconstruction errors by highlighting misjoins that can then be subjected to further investigation. Full article
(This article belongs to the Special Issue Assembly and Phasing of Complex Genomes in Plant)
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