Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain Article Swipe
Esther Camacho
,
Sandra González‐de la Fuente
,
José Carlos Solana
,
Alberto Rastrojo
,
Fernando Carrasco-Ramiro
,
José M. Requena
,
Begoña Aguado
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.3390/genes12091359
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.3390/genes12091359
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.
Related Topics
Concepts
Genome
Biology
Sequence assembly
Genome project
Genetics
Gene
Whole genome sequencing
Computational biology
Reference genome
Gene prediction
Shotgun sequencing
DNA sequencing
Gene Annotation
Hybrid genome assembly
Transcriptome
Gene expression
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/genes12091359
- https://www.mdpi.com/2073-4425/12/9/1359/pdf?version=1630504275
- OA Status
- gold
- Cited By
- 18
- References
- 75
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3196746572
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3196746572Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3390/genes12091359Digital Object Identifier
- Title
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Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin StrainWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-08-29Full publication date if available
- Authors
-
Esther Camacho, Sandra González‐de la Fuente, José Carlos Solana, Alberto Rastrojo, Fernando Carrasco-Ramiro, José M. Requena, Begoña AguadoList of authors in order
- Landing page
-
https://doi.org/10.3390/genes12091359Publisher landing page
- PDF URL
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https://www.mdpi.com/2073-4425/12/9/1359/pdf?version=1630504275Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://www.mdpi.com/2073-4425/12/9/1359/pdf?version=1630504275Direct OA link when available
- Concepts
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Genome, Biology, Sequence assembly, Genome project, Genetics, Gene, Whole genome sequencing, Computational biology, Reference genome, Gene prediction, Shotgun sequencing, DNA sequencing, Gene Annotation, Hybrid genome assembly, Transcriptome, Gene expressionTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
18Total citation count in OpenAlex
- Citations by year (recent)
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2025: 7, 2024: 3, 2023: 4, 2022: 4Per-year citation counts (last 5 years)
- References (count)
-
75Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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