ena-STUDY-CBMSO-09-04-2018-07:54:09:533-4006
Genome sequence and transcriptome for the Friedlin strain of Leishmania major. For genomic DNA sequencing, two NGS methodologies were used: PacBio and Illumina. On the other hand, to define the transcriptome, total poly-A+ RNA was sequenced using Illumina HiSeq 2000 technology.
This project was aimed to determine the genome sequence and transcriptome for the Friedlin strain of Leishmania major, a parasitic protist, the causative agent of cutaneous leishmaniasis (CL), a disease affecting yearly around 1.5 million people worldwide. This species was chosen for sequencing the first genome for a species of the genus Leishmania. In particular, the Friedlin strain was selected for this purpose, and the sequence was published in 2005 (Ivens 2005. Science 309:436). Although this genome assembly represents one of the more solid genomes assembled to date for Leishmania, the existence of some misassembled genomic regions was evidenced recently (Alonso et al. 2016. Parasites & vectors 9:74). Taking into accountConsidering the tremendous advances achieved in sequencing techniques, we undertook the objective of de novo assembling of the genome for this L. major strain using sequence reads generated by two different NGS platforms, Illumina and PacBio. These sequence reads were used to assemble the complete genome, composed ofby 36 chromosomes per haploid set. Afterwards, gene annotation (CDS for protein coding-genes and structural RNAs) was carried out by a combination of automated procedures and manual revision. On the other hand, to define the transcriptome, total poly-A+ RNA was sequenced using Illumina HiSeq 2000 technology. After transcript assembly, the boundaries of transcripts were determined by mapping spliced-leader (5'-end) and poly-A (3'-end) addition sites. As a result, in this project, we are providing the following data:- PacBio and Illumina sequence reads from genomic DNA.- Illumina reads from polyA+ RNA (RNAseq)- Nucleotide sequence of the 36 chromosomes.- Annotation data for transcripts, CDS, structural RNAs (rRNAs, tRNAs and snoRNAs).
This project was aimed to determine the genome sequence and transcriptome for the Friedlin strain of Leishmania major, a parasitic protist, the causative agent of cutaneous leishmaniasis (CL), a disease affecting yearly around 1.5 million people worldwide. This species was chosen for sequencing the first genome for a species of the genus Leishmania. In particular, the Friedlin strain was selected for this purpose, and the sequence was published in 2005 (Ivens 2005. Science 309:436). Although this genome assembly represents one of the more solid genomes assembled to date for Leishmania, the existence of some misassembled genomic regions was evidenced recently (Alonso et al. 2016. Parasites & vectors 9:74). Taking into accountConsidering the tremendous advances achieved in sequencing techniques, we undertook the objective of de novo assembling of the genome for this L. major strain using sequence reads generated by two different NGS platforms, Illumina and PacBio. These sequence reads were used to assemble the complete genome, composed ofby 36 chromosomes per haploid set. Afterwards, gene annotation (CDS for protein coding-genes and structural RNAs) was carried out by a combination of automated procedures and manual revision. On the other hand, to define the transcriptome, total poly-A+ RNA was sequenced using Illumina HiSeq 2000 technology. After transcript assembly, the boundaries of transcripts were determined by mapping spliced-leader (5'-end) and poly-A (3'-end) addition sites. As a result, in this project, we are providing the following data:- PacBio and Illumina sequence reads from genomic DNA.- Illumina reads from polyA+ RNA (RNAseq)- Nucleotide sequence of the 36 chromosomes.- Annotation data for transcripts, CDS, structural RNAs (rRNAs, tRNAs and snoRNAs).