Special Issue "Applications of Bioinformatics in Plant Resources and Omics"
Deadline for manuscript submissions: 15 January 2024 | Viewed by 24755
Interests: bioinformatics; plant genomics; transcriptomics; annotation; bioinformatics tools; olive; avocado; mango
Special Issues, Collections and Topics in MDPI journals
Interests: transcriptomics; next generation sequencing; genomics; bioinformatics and computational biology; gene expression; bioinformatics; sequencing; DNA computational biology; DNA sequencing; plant abiotic stress; pollen allergens
Special Issues, Collections and Topics in MDPI journals
The advances in sequencing technologies and genome assembly methods that do not require genetic maps to generate chromosome-scale genome references are generating a plethora of genome sequences in plants, especially for non-model species. Today, projects to sequence thousands of plant transcriptomes and genomes are in progress, and many bioinformatics tools have been developed and applied for omics plant research. These advances are allowing us to access a great number of useful resources and bioinformatics tools to study plants, in some cases in species which had few or even no omics data before. This Special Issue of Plants aims to highlight omics resources produced for plants, such as genomes, transcriptomes, gene expression data, gene or genome annotations, metabolomes, proteomes, epigenomes, and metagenomes of microorganisms interacting with plants, and bioinformatics tools used or developed to generate these resources, such as analysis tools, automated pipelines, databases or web tools.
Dr. Noe Fernandez-Pozo
Prof. Dr. M. Gonzalo Claros
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.
- bioinformatics tools
- alternative splicing
- functional analysis
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Paper 1: Title: Olive Genome Structure, Evolution And Domestication
Cultivated plants frequently present complex genomes as a result of autopolyploidy and sometimes as interspecies hybrids polyploids. This makes it difficult to assemble good genomes for these plants and represent a scientific challenge. In this review, we describe the present knowledge of the olive genome, one of these complex genomes of cultivated plants. The olive genome also contains structural clues to understand the evolution of this specie and its domestication. Indeed, there are differences in the few genomes assembled regarding the size of the nuclear genome and the number of genes. However, what seems to be clear is that the olive the olive genome appears to have undergone two ancestral whole genome duplication events, around 57-63 and 25-28 millions of years. A very relevant fact is that during the Holocene the transposons have been massive activated, which can explain at least part of the high genetic variability of the cultivated olive tree. Analysis of several olive genomes supports the hypothesis of two main domestication events, although the possibility of a single main event cannot be ruled out. However, probably due to the high admixture of most of the olive varieties, it is difficult to establish a precise origin for the current olive varieties.
Keywords: Olea europaea, genome, domestication, transposons, genetic variability
Paper 2: MangoBase: a genomics portal and gene expression atlas for Mangifera indica
Paper 3:OliveAtlas: A gene expression atlas for Olea Europaea
Paper 4: Prospective study of olive pollen tube development revealing transcription factors and RING proteins involved in functional changes.
Evolutionary dynamics of FLC-like MADS-box genes in flowering plants
MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which the ones with functions in the specification of floral organ identity are especially known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants. i) FLC-like genes are under heavy epigenetic control not only including transcription factors, but also long non-coding RNAs in sense and antisense orientation, and massiv histone modifications. ii) FLC-like genes undergo considerable alternative splicing, at least some of which is of functional importance, e.g. in temperature-sensitive flowering. iii) FLC-like genes, especially MAF-like genes, show an unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. iv) FLC-like genes are among the few clades of MIKC-type MADS-box genes that have got lost completely in some lineages of flowering plants. Here we make use of the latest genomic data of angiosperms to study these remarkable features of the FLC-like genes in a phylogenetic context. We estimate the rate of tandem duplications and provide a hypothesis as to when different epigentic regulatory mechanisms originated during evolution.
Key words: alternative splicing, long non-coding RNAs, epigenetic regulation, MADS-box gene, phylogenomic, comparative transcriptomics, transcription factor