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Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (15 February 2022) | Viewed by 30139

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Special Issue Editors

Prof. Dr. Yuriy L. Orlov

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Guest Editor

The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
Interests: computer genomics; bioinformatics; digital medicine (e-Health); gene expression regulation; ChIP-seq
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Prof. Dr. Ming Chen

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Guest Editor

College of Life Sciences, Zhejiang University, Hangzhou 310058, China
Interests: bioinformatics; systems biology
Special Issues, Collections and Topics in MDPI journals

Dr. Oxana B. Dobrovolskaya

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Guest Editor

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Interests: plant genetics; plant physiology; wheat; bioinformatics; biotechnology

Special Issue Information

Dear Colleagues,

The study of molecular mechanisms of plant stress response is important for agrobiotechnology applications. It is in the focus of modern sequencing and bioinformatics research. Sequencing and systems biology approaches offer a comprehensive view of plant growth from molecular to cellular, organ, and population levels. Sequencing and microscopy technologies make it possible to model protein–protein and gene regulatory interactions in plant cells, providing a basis for better crop production and sustainability. Plant–pathogen interaction studies complement network modeling in this area. Based on the high demand, we announce this Special Issue on molecular informatics for plant biotechnology, continuing journal Special Issues on medical genomics and bioinformatics based on sequencing data analysis.

In this Special Issue we collect works on the following topics: 1) gene expression regulation in plants; 2) plant genomics and bioinformatics; 3) miRNA and molecular mechanisms studies in plants; 4) plant systems biology and digital phenotyping; 5) sequencing of model organisms for agro- and biotechnology.

The materials presented at Plantgen-21 conference (14-18 June 2021, Novosibirsk, Russia, https://conf.icgbio.ru/plantgen2021/) are welcome!

Prof. Dr. Yuriy L. Orlov
Prof. Dr. Ming Chen
Dr. Oxana B. Dobrovolskaya
Guest Editors

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Keywords

gene expression regulation in plants
molecular mechanisms of stress resistance in plants
ncRNA and gene editing in plants
plant–pathogen interactions
systems biology for agrobiology
next-generation sequencing in biotechnology
transcriptome analysis in plants
modeling of plant cell growth
gene networks in plants
digital applications in plant phenotyping

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Published Papers (9 papers)

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Editorial

Jump to: Research, Review

4 pages, 224 KiB

Open AccessEditorial

Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics

by Yuriy L. Orlov, Vladimir A. Ivanisenko, Oxana B. Dobrovolskaya and Ming Chen

Int. J. Mol. Sci. 2022, 23(12), 6759; https://doi.org/10.3390/ijms23126759 - 17 Jun 2022

Cited by 5 | Viewed by 2685

Abstract

The study of molecular mechanisms of plant stress response is important for agrobiotechnology applications as it was discussed at series of recent bioinformatics conferences [...] Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

Research

Jump to: Editorial, Review

20 pages, 6030 KiB

Open AccessArticle

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

by Aleksandr V. Bobrovskikh, Ulyana S. Zubairova, Eugeniya I. Bondar, Viktoriya V. Lavrekha and Alexey V. Doroshkov

Int. J. Mol. Sci. 2022, 23(8), 4455; https://doi.org/10.3390/ijms23084455 - 18 Apr 2022

Cited by 8 | Viewed by 3606

Abstract

The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in Arabidopsis thaliana L. using resources GEO NCBI, string-db, ShinyGO, STREME, and Tomtom, as well as programs metaRE, CisCross, and Cytoscape. Through the meta-analysis of five transcriptomic experiments, we selected a set of 1151 differentially expressed genes, including 453 genes that compose the gene network. Ten significantly enriched regulatory motifs for TFs families ZF-HD, HB, C2H2, NAC, BZR, and ARID were found in the promoter regions of differentially expressed genes. In addition, we predicted families of transcription factors associated with the duration of exposure (RAV, HSF), intensity of high light treatment (MYB, REM), and the direction of gene expression change (HSF, S1Fa-like). We predicted genetic components systems involved in a high light response and their expression changes, potential transcriptional regulators, and associated processes. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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11 pages, 2720 KiB

Open AccessArticle

ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data

by Huan Qi, Xiaokun Guo, Tianpeng Wang and Ziding Zhang

Int. J. Mol. Sci. 2022, 23(8), 4079; https://doi.org/10.3390/ijms23084079 - 7 Apr 2022

Cited by 6 | Viewed by 3432

Abstract

Alternative splicing (AS) is an essential co-transcriptional regulatory mechanism in eukaryotes. The accumulation of plant RNA-Seq data provides an unprecedented opportunity to investigate the global landscape of plant AS events. However, most existing AS identification tools were originally designed for animals, and their performance in plants was not rigorously benchmarked. In this work, we developed a simple and easy-to-use bioinformatics tool named ASTool for detecting AS events from plant RNA-Seq data. As an exon-based method, ASTool can detect 4 major AS types, including intron retention (IR), exon skipping (ES), alternative 5′ splice sites (A5SS), and alternative 3′ splice sites (A3SS). Compared with existing tools, ASTool revealed a favorable performance when tested in simulated RNA-Seq data, with both recall and precision values exceeding 95% in most cases. Moreover, ASTool also showed a competitive computational speed and consistent detection results with existing tools when tested in simulated or real plant RNA-Seq data. Considering that IR is the most predominant AS type in plants, ASTool allowed the detection and visualization of novel IR events based on known splice sites. To fully present the functionality of ASTool, we also provided an application example of ASTool in processing real RNA-Seq data of Arabidopsis in response to heat stress. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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19 pages, 6284 KiB

Open AccessArticle

Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers

by Jana Zwyrtková, Nicolas Blavet, Alžběta Doležalová, Petr Cápal, Mahmoud Said, István Molnár, Jan Vrána, Jaroslav Doležel and Eva Hřibová

Int. J. Mol. Sci. 2022, 23(6), 3191; https://doi.org/10.3390/ijms23063191 - 16 Mar 2022

Cited by 5 | Viewed by 2743

Abstract

Crested wheatgrass (Agropyron cristatum), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Its wider use is hampered by limited knowledge of its complex genome. In this work, individual chromosomes were purified by flow sorting, and DNA shotgun sequencing was performed. The annotation of chromosome-specific sequences characterized the DNA-repeat content and led to the identification of genic sequences. Among them, genic sequences homologous to genes conferring plant disease resistance and involved in plant tolerance to biotic and abiotic stress were identified. Genes belonging to the important groups for breeders involved in different functional categories were found. The analysis of the DNA-repeat content identified a new LTR element, Agrocen, which is enriched in centromeric regions. The colocalization of the element with the centromeric histone H3 variant CENH3 suggested its functional role in the grass centromere. Finally, 159 polymorphic simple-sequence-repeat (SSR) markers were identified, with 72 of them being chromosome- or chromosome-arm-specific, 16 mapping to more than one chromosome, and 71 mapping to all the Agropyron chromosomes. The markers were used to characterize orthologous relationships between A. cristatum and common wheat that will facilitate the introgression breeding of wheat using A. cristatum. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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23 pages, 11122 KiB

Open AccessArticle

Deciphering the Host–Pathogen Interactome of the Wheat–Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat

by Raghav Kataria and Rakesh Kaundal

Int. J. Mol. Sci. 2022, 23(5), 2589; https://doi.org/10.3390/ijms23052589 - 26 Feb 2022

Cited by 10 | Viewed by 3101

Abstract

Common bunt, caused by two fungal species, Tilletia caries and Tilletia laevis, is one of the most potentially destructive diseases of wheat. Despite the availability of synthetic chemicals against the disease, organic agriculture relies greatly on resistant cultivars. Using two computational approaches—interolog and domain-based methods—a total of approximately 58 M and 56 M probable PPIs were predicted in T. aestivum–T. caries and T. aestivum–T. laevis interactomes, respectively. We also identified 648 and 575 effectors in the interactions from T. caries and T. laevis, respectively. The major host hubs belonged to the serine/threonine protein kinase, hsp70, and mitogen-activated protein kinase families, which are actively involved in plant immune signaling during stress conditions. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the host proteins revealed significant GO terms (O-methyltransferase activity, regulation of response to stimulus, and plastid envelope) and pathways (NF-kappa B signaling and the MAPK signaling pathway) related to plant defense against pathogens. Subcellular localization suggested that most of the pathogen proteins target the host in the plastid. Furthermore, a comparison between unique T. caries and T. laevis proteins was carried out. We also identified novel host candidates that are resistant to disease. Additionally, the host proteins that serve as transcription factors were also predicted. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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15 pages, 2626 KiB

Open AccessArticle

Population Analysis of Diospyros lotus in the Northwestern Caucasus Based on Leaf Morphology and Multilocus DNA Markers

by Lidia S. Samarina, Valentina I. Malyarovskaya, Ruslan S. Rakhmangulov, Natalia G. Koninskaya, Alexandra O. Matskiv, Ruset M. Shkhalakhova, Yuriy L. Orlov, Gregory A. Tsaturyan, Ekaterina S. Shurkina, Maya V. Gvasaliya, Alexandr S. Kuleshov and Alexey V. Ryndin

Int. J. Mol. Sci. 2022, 23(4), 2192; https://doi.org/10.3390/ijms23042192 - 16 Feb 2022

Cited by 3 | Viewed by 2394

Abstract

Diospyros lotus is the one of the most frost-tolerant species in the Diospyros genera, used as a rootstock for colder regions. Natural populations of D. lotus have a fragmented character of distribution in the Northwestern Caucasus, one of the coldest regions of Diospyros cultivation. To predict the behavior of D. lotus populations in an extreme environment, it is necessary to investigate the intraspecific genetic diversity and phenotypic variability of populations in the colder regions. In this study, we analyzed five geographically distant populations of D. lotus according to 33 morphological leaf traits, and the most informative traits were established, namely, leaf length, leaf width, leaf index (leaf to length ratio) and the length of the fourth veins. Additionally, we evaluated the intraspecific genetic diversity of D. lotus using ISSR and SCoT markers and proposed a new parameter for the evaluation of genetic polymorphism among populations, in order to eliminate the effect of sample number. This new parameter is the relative genetic polymorphism, which is the ratio of polymorphism to the number of samples. Based on morphological and genetic data, the northernmost population from Shkhafit was phenotypically and genetically distant from the other populations. The correspondence between several morphological traits (leaf width, leaf length and first to fifth right vein angles) and several marker bands (SCoT5, SCoT7, SCoT30: 800–1500 bp; ISSR13, ISSR14, ISSR880: 500–1000 bp) were observed for the Shkhafit population. Unique SCoT and ISSR fragments can be used as markers for breeding purposes. The results provide a better understanding of adaptive mechanisms in D. lotus in extreme environments and will be important for the further expansion of the cultivation area for persimmon in colder regions. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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16 pages, 15635 KiB

Open AccessArticle

Genome-Wide Prediction of Transcription Start Sites in Conifers

by Eugeniya I. Bondar, Maxim E. Troukhan, Konstantin V. Krutovsky and Tatiana V. Tatarinova

Int. J. Mol. Sci. 2022, 23(3), 1735; https://doi.org/10.3390/ijms23031735 - 3 Feb 2022

Cited by 4 | Viewed by 3317

Abstract

The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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15 pages, 1403 KiB

Open AccessArticle

Genomic Regions Associated with Fusarium Wilt Resistance in Flax

by Alexander Kanapin, Mikhail Bankin, Tatyana Rozhmina, Anastasia Samsonova and Maria Samsonova

Int. J. Mol. Sci. 2021, 22(22), 12383; https://doi.org/10.3390/ijms222212383 - 17 Nov 2021

Cited by 11 | Viewed by 2302

Abstract

Modern flax cultivars are susceptible to many diseases; arguably, the most economically damaging of these is the Fusarium wilt fungal disease. Over the past decades international flax breeding initiatives resulted in the development of resistant cultivars. However, much remains to be learned about the mechanisms of resistance to Fusarium infection in flax. As a first step to uncover the genetic factors associated with resistance to Fusarium wilt disease, we performed a genome-wide association study (GWAS) using 297 accessions from the collection of the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. These genotypes were infected with a highly pathogenic Fusarium oxysporum f.sp. lini MI39 strain; the wilt symptoms were documented in the course of three successive years. Six different single-locus models implemented in GAPIT3 R package were applied to a selected subset of 72,526 SNPs. A total of 15 QTNs (Quantitative Trait Nucleotides) were detected during at least two years of observation, while eight QTNs were found during all three years of the experiment. Of these, ten QTNs occupied a region of 640 Kb at the start of chromosome 1, while the remaining QTNs mapped to chromosomes 8, 11 and 13. All stable QTNs demonstrate a statistically significant allelic effect across 3 years of the experiment. Importantly, several QTNs spanned regions that harbored genes involved in the pathogen recognition and plant immunity response, including the KIP1-like protein (Lus10025717) and NBS-LRR protein (Lus10025852). Our results provide novel insights into the genetic architecture of flax resistance to Fusarium wilt and pinpoint potential candidate genes for further in-depth studies. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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Review

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23 pages, 3669 KiB

Open AccessReview

Optogenetic and Chemical Induction Systems for Regulation of Transgene Expression in Plants: Use in Basic and Applied Research

by Evgeniya S. Omelina, Anastasiya A. Yushkova, Daria M. Motorina, Grigorii A. Volegov, Elena N. Kozhevnikova and Alexey V. Pindyurin

Int. J. Mol. Sci. 2022, 23(3), 1737; https://doi.org/10.3390/ijms23031737 - 3 Feb 2022

Cited by 13 | Viewed by 4658

Abstract

Continuous and ubiquitous expression of foreign genes sometimes results in harmful effects on the growth, development and metabolic activities of plants. Tissue-specific promoters help to overcome this disadvantage, but do not allow one to precisely control transgene expression over time. Thus, inducible transgene expression systems have obvious benefits. In plants, transcriptional regulation is usually driven by chemical agents under the control of chemically-inducible promoters. These systems are diverse, but usually contain two elements, the chimeric transcription factor and the reporter gene. The commonly used chemically-induced expression systems are tetracycline-, steroid-, insecticide-, copper-, and ethanol-regulated. Unlike chemical-inducible systems, optogenetic tools enable spatiotemporal, quantitative and reversible control over transgene expression with light, overcoming limitations of chemically-inducible systems. This review updates and summarizes optogenetic and chemical induction methods of transgene expression used in basic plant research and discusses their potential in field applications. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)

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