Genetics and Proteogenomics of Kinetoplastids

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 2586

Special Issue Editor


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Guest Editor
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid, 28049 Madrid, Spain
Interests: Leishmania; Trypanosoma; heat shock proteins; RNA binding proteins; regulation of gene expression; genomics; transcriptomics
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Special Issue Information

Dear Colleagues,

We are proud to announce the opening of a second volume dealing with the genetics and genomics of kinetoplastids, following the great success of the previous volume and the interest it attracted among researchers working in the field of these astonishing microorganisms. You can access the contributions appearing in the first volume at https://www.mdpi.com/books/pdfview/book/4005

Kinetoplastid protists belong to the Euglenozoa phylum and represent one of the earliest extant branches of eukaryotic lineage. This is one of the most successful groups of live beings. Apart from the trypanosomatids causing human diseases (e.g., Trypanosoma ssp., causing Chagas disease and sleeping sickness in humans, and Leishmania spp., causing kala-azar and other leishmaniases),  many parasites for plants (Phytomonas spp.) and insects (LeptomonasAngomonas, Crithidia, and other genera) also belong to this class. In addition, free-living kinetoplastids (Bodo spp.) are abundant and active microbial predators in terrestrial and aquatic ecosystems.

In recent years, the incorporation of “omics” methodologies to the study of these organisms has allowed the assembly of genomes for a growing number of both parasitic and free-living kinetoplastids to analyze changes in gene expression, determine the proteome compendium, establish metabolic pathways, and so on. Therefore, a vast amount of genetics and genomics data are being generated that will contribute to increasing our knowledge on the peculiar aspects of cytology, genome organization, and mechanisms of gene regulation that this group of organisms have evolved since their ancient evolutionary origin.

The aim of this Special Issue is to bring together a set of reviews and research articles addressing aspects such as genome organization, mechanisms of gene expression, specific metabolic pathways, evolutionary relationships and databases, among others, focused on any species belonging to this group of protists.

Dr. Jose María Requena
Guest Editor

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Keywords

  • kinetoplastids
  • genome assembly and annotation
  • transcriptomics and regulation and gene expression
  • proteomics
  • metabolomics
  • phylogenetics
  • databases and web resources
  • mechanisms of drug resistance
  • virulence factors

Published Papers (1 paper)

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Research

18 pages, 4333 KiB  
Article
Nanopore-Based Direct RNA Sequencing of the Trypanosoma brucei Transcriptome Identifies Novel lncRNAs
by Elisabeth Kruse and H. Ulrich Göringer
Genes 2023, 14(3), 610; https://doi.org/10.3390/genes14030610 - 28 Feb 2023
Cited by 2 | Viewed by 2146
Abstract
Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression post-transcriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay, to translation, in addition to a large panel of [...] Read more.
Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression post-transcriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay, to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized to date. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known, because of the inherent cDNA-recoding and DNA-amplification limitations of short-read RNA sequencing. Here, we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosome Trypanosoma brucei, with a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 32 of which are stage-specifically expressed. We also present insights into the complexity of the T. brucei transcriptome, including alternative transcriptional start and stop sites and potential transcript isoforms, to provide a bias-free understanding of the intricate RNA landscape in T. brucei. Full article
(This article belongs to the Special Issue Genetics and Proteogenomics of Kinetoplastids)
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