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In this study, a complete assembly of the genome of <jats:italic>L<\/jats:italic>. <jats:italic>donovani<\/jats:italic> is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an <jats:italic>L<\/jats:italic>. <jats:italic>donovani<\/jats:italic> genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A\u2009+\u2009RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of <jats:italic>cis-<\/jats:italic>splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.<\/jats:p>","DOI":"10.1038\/s41598-019-42511-4","type":"journal-article","created":{"date-parts":[[2019,4,16]],"date-time":"2019-04-16T10:03:21Z","timestamp":1555409001000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation"],"prefix":"10.1038","volume":"9","author":[{"given":"Esther","family":"Camacho","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Gonz\u00e1lez-de la Fuente","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"Rastrojo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2450-2999","authenticated-orcid":false,"given":"Ram\u00f3n","family":"Peir\u00f3-Pastor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Carlos","family":"Solana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Tabera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Gamarro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Carrasco-Ramiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7550-0198","authenticated-orcid":false,"given":"Jose M.","family":"Requena","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bego\u00f1a","family":"Aguado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,4,16]]},"reference":[{"key":"42511_CR1","doi-asserted-by":"publisher","first-page":"1861","DOI":"10.1099\/ijs.0.63081-0","volume":"54","author":"D Moreira","year":"2004","unstructured":"Moreira, D., Lopez-Garcia, P. & Vickerman, K. 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