Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations

Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotat...

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Autores: Camacho Cano, Esther, González-de la Fuente, Sandra, Solana Morcillo, José Carlos, Tabera, Laura, Carrasco-Ramiro, Fernando, Aguado Orea, Begoña, Requena Rolania, José María
Tipo de documento: artigo
Data de publicação:2023
País:España
Recursos:Universidad Autónoma de Madrid
Repositório:Biblos-e Archivo. Repositorio Institucional de la UAM
Idioma:inglês
OAI Identifier:oai:repositorio.uam.es:10486/707685
Acesso em linha:http://hdl.handle.net/10486/707685
https://dx.doi.org/10.3390/genes14040866
Access Level:Acceso aberto
Palavra-chave:Polyadenylic Acid
RNA
Transcriptome
Heterozygosity
Molecular Genetics
Genetic Heterogeneity
Biología y Biomedicina / Biología
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spelling Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotationsCamacho Cano, EstherGonzález-de la Fuente, SandraSolana Morcillo, José CarlosTabera, LauraCarrasco-Ramiro, FernandoAguado Orea, BegoñaRequena Rolania, José MaríaPolyadenylic AcidRNATranscriptomeHeterozygosityMolecular GeneticsGenetic HeterogeneityBiología y Biomedicina / BiologíaLeishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteinsThis research was supported by the Spanish Ministerio de Ciencia, Innovación (MICINN), Agencia Estatal deInvestigación(AEI), grant number PID2020-117916RB-I00, and Instituto de Salud Carlos III, grant CB21/13/00018 (CIBERINFEC). An institutional grant from Fundacion RamonAreces is also acknowledgedMDPIDepartamento de Biología MolecularFacultad de Ciencias20232023-04-01research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/707685https://dx.doi.org/10.3390/genes14040866reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/7076852026-06-23T12:46:27Z
dc.title.none.fl_str_mv Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
title Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
spellingShingle Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
Camacho Cano, Esther
Polyadenylic Acid
RNA
Transcriptome
Heterozygosity
Molecular Genetics
Genetic Heterogeneity
Biología y Biomedicina / Biología
title_short Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
title_full Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
title_fullStr Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
title_full_unstemmed Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
title_sort Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations
dc.creator.none.fl_str_mv Camacho Cano, Esther
González-de la Fuente, Sandra
Solana Morcillo, José Carlos
Tabera, Laura
Carrasco-Ramiro, Fernando
Aguado Orea, Begoña
Requena Rolania, José María
author Camacho Cano, Esther
author_facet Camacho Cano, Esther
González-de la Fuente, Sandra
Solana Morcillo, José Carlos
Tabera, Laura
Carrasco-Ramiro, Fernando
Aguado Orea, Begoña
Requena Rolania, José María
author_role author
author2 González-de la Fuente, Sandra
Solana Morcillo, José Carlos
Tabera, Laura
Carrasco-Ramiro, Fernando
Aguado Orea, Begoña
Requena Rolania, José María
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Departamento de Biología Molecular
Facultad de Ciencias
dc.subject.none.fl_str_mv Polyadenylic Acid
RNA
Transcriptome
Heterozygosity
Molecular Genetics
Genetic Heterogeneity
Biología y Biomedicina / Biología
topic Polyadenylic Acid
RNA
Transcriptome
Heterozygosity
Molecular Genetics
Genetic Heterogeneity
Biología y Biomedicina / Biología
description Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteins
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-04-01
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10486/707685
https://dx.doi.org/10.3390/genes14040866
url http://hdl.handle.net/10486/707685
https://dx.doi.org/10.3390/genes14040866
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Biblos-e Archivo. Repositorio Institucional de la UAM
instname:Universidad Autónoma de Madrid
instname_str Universidad Autónoma de Madrid
reponame_str Biblos-e Archivo. Repositorio Institucional de la UAM
collection Biblos-e Archivo. Repositorio Institucional de la UAM
repository.name.fl_str_mv
repository.mail.fl_str_mv
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