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Plants
Special Issues
Harnessing the Power of Genome and Transcriptome Assemblies
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Harnessing the Power of Genome and Transcriptome Assemblies

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 (30 April 2021) | Viewed by 9435

Special Issue Editor

Dr. Boas Pucker

E-Mail Website
Guest Editor
Department of Plant Sciences, University of Cambridge, Cambridge, UK
Interests: genome assembly; long-read sequencing; bioinformatics; genome evolution; specialised metabolism; evolution of betalain and flavonoid biosynthesis; MYB transcription factors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

The availability of high-quality genome and transcriptome assemblies is crucial for numerous studies of specific plant functions. Long-read sequencing technologies boost the contiguity of genome assemblies and open up novel opportunities in plant transcriptomics.

Chromosome-scale plant genome assemblies can be harnessed for the discovery of metabolic networks, in the identification of genetic loci underlying agronomic traits, to support breeding programs, or to study genetic diversity. The evolutionary history of plants is recorded in their genome structure and can be revealed through sequencing, assembly, and comparison of genome sequences. Current sequencing technologies reveal methylation patterns and other DNA modifications in addition to genome sequences.

Transcriptome assemblies are a cost-effective way to access the genes of plant species with large and complex genomes. Direct RNA sequencing allows the identification of modifications on these transcripts. Deep sequencing with long reads enables detailed investigations of splicing processes, leading to a huge variety of transcript isoforms.

This Special Issue is open to all research articles providing new insights into the biology of plants based on genome or transcriptome assemblies.

Particularly welcome are research papers on the following topics:

  • Genome or transcriptome assemblies of potential crop species (orphan crops);
  • Re-sequencing studies addressing variability in plant genomes;
  • Mapping-by-sequencing studies with a focus on agronomic traits;
  • Investigations of metabolic pathways, networks, or gene families based on genome or transcriptome assemblies;
  • Transcriptome analyses of specific tissues, cell types, or conditions;
  • Bioinformatic approaches advancing the field of plant genomics.

Dr. Boas Pucker
Guest Editor

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

  • genome assembly
  • transcriptome assembly
  • long read sequencing
  • Oxford Nanopore Technologies (ONT)
  • Pacific Biosciences (PacBio)
  • RNA-Seq
  • RNA sequencing
  • genome evolution
  • genome mining
  • crop genomics
  • plant breeding
  • gene expression
  • genome skimming
  • mapping-by-sequencing (MBS)
  • cross-species transcriptomics
  • functional genomics
  • structural variations
  • metabolic gene clusters
  • marker-assisted selection

Published Papers (3 papers)

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Research

20 pages, 7351 KiB  
Article
Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum
by Christian Siadjeu, Eike Mayland-Quellhorst, Shruti Pande, Sascha Laubinger and Dirk C. Albach
Plants 2021, 10(4), 787; https://doi.org/10.3390/plants10040787 - 16 Apr 2021
Cited by 7 | Viewed by 3103
Abstract
Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in [...] Read more.
Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH. Full article
(This article belongs to the Special Issue Harnessing the Power of Genome and Transcriptome Assemblies)
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22 pages, 1811 KiB  
Article
Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies
by Ashwil Klein, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar and David L. Tabb
Plants 2021, 10(4), 765; https://doi.org/10.3390/plants10040765 - 14 Apr 2021
Cited by 1 | Viewed by 2429
Abstract
While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments [...] Read more.
While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity “genes” varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome. Full article
(This article belongs to the Special Issue Harnessing the Power of Genome and Transcriptome Assemblies)
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16 pages, 3033 KiB  
Article
Genome-Wide Discovery of InDel Markers in Sesame (Sesamum indicum L.) Using ddRADSeq
by Sibel Kizil, Merve Basak, Birgul Guden, Hilal Sule Tosun, Bulent Uzun and Engin Yol
Plants 2020, 9(10), 1262; https://doi.org/10.3390/plants9101262 - 24 Sep 2020
Cited by 17 | Viewed by 3098
Abstract
The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic [...] Read more.
The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1–2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3′- and 5′- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders. Full article
(This article belongs to the Special Issue Harnessing the Power of Genome and Transcriptome Assemblies)
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