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Article

Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Centro de Biología Molecular “Severo Ochoa” (CBMSO, CSIC-UAM), Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Academic Editor: Sam Alsford
Genes 2021, 12(9), 1359; https://doi.org/10.3390/genes12091359
Received: 3 July 2021 / Revised: 20 August 2021 / Accepted: 27 August 2021 / Published: 29 August 2021
(This article belongs to the Special Issue Genetics and Genomics of Leishmania)
Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain. View Full-Text
Keywords: genome; transcriptome; gene models; Leishmania; Illumina sequencing; PacBio sequencing; expression levels; untranslated regions (UTR); SL-additions site (SAS); polyadenylation site (PAS) genome; transcriptome; gene models; Leishmania; Illumina sequencing; PacBio sequencing; expression levels; untranslated regions (UTR); SL-additions site (SAS); polyadenylation site (PAS)
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MDPI and ACS Style

Camacho, E.; González-de la Fuente, S.; Solana, J.C.; Rastrojo, A.; Carrasco-Ramiro, F.; Requena, J.M.; Aguado, B. Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain. Genes 2021, 12, 1359. https://doi.org/10.3390/genes12091359

AMA Style

Camacho E, González-de la Fuente S, Solana JC, Rastrojo A, Carrasco-Ramiro F, Requena JM, Aguado B. Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain. Genes. 2021; 12(9):1359. https://doi.org/10.3390/genes12091359

Chicago/Turabian Style

Camacho, Esther, Sandra González-de la Fuente, Jose C. Solana, Alberto Rastrojo, Fernando Carrasco-Ramiro, Jose M. Requena, and Begoña Aguado. 2021. "Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain" Genes 12, no. 9: 1359. https://doi.org/10.3390/genes12091359

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