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Plants
Special Issues
Assembly and Phasing of Complex Genomes in Plant
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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 2547

Special Issue Editors

Prof. Dr. Xingtan Zhang

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

E-Mail Website
Guest Editor
College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
Interests: bioinformatics; plant genomics; evolution
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Won C. Yim

E-Mail Website
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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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://0-doi-org.brum.beds.ac.uk/10.3390/plants12020320 - 10 Jan 2023
Viewed by 1949
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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