Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation
Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L . donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L . d...
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| Veröffentlicht in: | Scientific reports 2019-04, Vol.9 (1), p.6127-6127, Article 6127 |
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| creator | Camacho, Esther González-de la Fuente, Sandra Rastrojo, Alberto Peiró-Pastor, Ramón Solana, Jose Carlos Tabera, Laura Gamarro, Francisco Carrasco-Ramiro, Fernando Requena, Jose M. Aguado, Begoña |
| description | Leishmania donovani
is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of
L
.
donovani
is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an
L
.
donovani
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 + RNA, 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
cis-
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. |
| doi_str_mv | 10.1038/s41598-019-42511-4 |
| format | Article |
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is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of
L
.
donovani
is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an
L
.
donovani
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 + RNA, 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
cis-
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.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-019-42511-4</identifier><identifier>PMID: 30992521</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>38/23 ; 38/39 ; 38/43 ; 38/77 ; 38/91 ; 45 ; 45/90 ; 631/326/417/2551 ; 631/337/2019 ; Antiprotozoal Agents - pharmacology ; Antiprotozoal Agents - therapeutic use ; Chromosomes ; Chromosomes - genetics ; Drug Resistance, Microbial - genetics ; Gene expression ; Genome, Protozoan - genetics ; Genomes ; Heterogeneity ; Humanities and Social Sciences ; Humans ; Leishmania donovani ; Leishmania donovani - genetics ; Leishmaniasis, Visceral - drug therapy ; Leishmaniasis, Visceral - parasitology ; Molecular Sequence Annotation ; multidisciplinary ; Parasites ; Ribonucleic acid ; RNA ; RNA-Seq ; Science ; Science (multidisciplinary) ; Splicing ; Transcriptome - genetics ; Tropism ; Vector-borne diseases ; Visceral leishmaniasis</subject><ispartof>Scientific reports, 2019-04, Vol.9 (1), p.6127-6127, Article 6127</ispartof><rights>The Author(s) 2019</rights><rights>The Author(s) 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c511t-b432d95d867941f5ab52b1c621b676cc1eaa41a44fc6c2bf0bbc73f45ef250ab3</citedby><cites>FETCH-LOGICAL-c511t-b432d95d867941f5ab52b1c621b676cc1eaa41a44fc6c2bf0bbc73f45ef250ab3</cites><orcidid>0000-0003-2450-2999 ; 0000-0001-7550-0198</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467909/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467909/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30992521$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Camacho, Esther</creatorcontrib><creatorcontrib>González-de la Fuente, Sandra</creatorcontrib><creatorcontrib>Rastrojo, Alberto</creatorcontrib><creatorcontrib>Peiró-Pastor, Ramón</creatorcontrib><creatorcontrib>Solana, Jose Carlos</creatorcontrib><creatorcontrib>Tabera, Laura</creatorcontrib><creatorcontrib>Gamarro, Francisco</creatorcontrib><creatorcontrib>Carrasco-Ramiro, Fernando</creatorcontrib><creatorcontrib>Requena, Jose M.</creatorcontrib><creatorcontrib>Aguado, Begoña</creatorcontrib><title>Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Leishmania donovani
is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of
L
.
donovani
is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an
L
.
donovani
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 + RNA, 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
cis-
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.</description><subject>38/23</subject><subject>38/39</subject><subject>38/43</subject><subject>38/77</subject><subject>38/91</subject><subject>45</subject><subject>45/90</subject><subject>631/326/417/2551</subject><subject>631/337/2019</subject><subject>Antiprotozoal Agents - pharmacology</subject><subject>Antiprotozoal Agents - therapeutic use</subject><subject>Chromosomes</subject><subject>Chromosomes - genetics</subject><subject>Drug Resistance, Microbial - genetics</subject><subject>Gene expression</subject><subject>Genome, Protozoan - genetics</subject><subject>Genomes</subject><subject>Heterogeneity</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Leishmania donovani</subject><subject>Leishmania donovani - genetics</subject><subject>Leishmaniasis, Visceral - drug therapy</subject><subject>Leishmaniasis, Visceral - parasitology</subject><subject>Molecular Sequence Annotation</subject><subject>multidisciplinary</subject><subject>Parasites</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA-Seq</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Splicing</subject><subject>Transcriptome - genetics</subject><subject>Tropism</subject><subject>Vector-borne diseases</subject><subject>Visceral leishmaniasis</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9UcFu1DAQtRCIVqU_wAFZ4tIeAvbYTtYXJLQCirQSl_ZYWbbj7LpK7MXOVurfM21KKRzwZUYzb9688SPkLWcfOBOrj1VypVcN47qRoDhv5AtyDEyqBgTAy2f5ETmt9YbhU6Al16_JkWBagwJ-TK7XedqPYQ7U1homN97RPNB5F-gmxLqbbIqW9jnlW8zo2cWVoHUuNqZzug0pTziXeoqVVH2J-3mppDzbOeb0hrwa7FjD6WM8IVdfv1yuL5rNj2_f1583jUflc-OkgF6rftV2KHBQ1ilw3LfAXdu13vNgreRWysG3HtzAnPOdGKQKAyhmnTghnxbe_cFNofchoaLR7EucbLkz2UbzdyfFndnmW9NKXMk0Epw9EpT88xDqbKZYfRhHm0I-VAPAmW47EB1C3_8DvcmHkvC8B5TEP2aAKFhQvuRaSxiexHBm7g00i4EGDTQPBhqJQ--en_E08tsuBIgFULGVtqH82f0f2l-Q_adZ</recordid><startdate>20190416</startdate><enddate>20190416</enddate><creator>Camacho, Esther</creator><creator>González-de la Fuente, Sandra</creator><creator>Rastrojo, Alberto</creator><creator>Peiró-Pastor, Ramón</creator><creator>Solana, Jose Carlos</creator><creator>Tabera, Laura</creator><creator>Gamarro, Francisco</creator><creator>Carrasco-Ramiro, Fernando</creator><creator>Requena, Jose M.</creator><creator>Aguado, Begoña</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-2450-2999</orcidid><orcidid>https://orcid.org/0000-0001-7550-0198</orcidid></search><sort><creationdate>20190416</creationdate><title>Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation</title><author>Camacho, Esther ; González-de la Fuente, Sandra ; Rastrojo, Alberto ; Peiró-Pastor, Ramón ; Solana, Jose Carlos ; Tabera, Laura ; Gamarro, Francisco ; Carrasco-Ramiro, Fernando ; Requena, Jose M. ; Aguado, Begoña</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c511t-b432d95d867941f5ab52b1c621b676cc1eaa41a44fc6c2bf0bbc73f45ef250ab3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>38/23</topic><topic>38/39</topic><topic>38/43</topic><topic>38/77</topic><topic>38/91</topic><topic>45</topic><topic>45/90</topic><topic>631/326/417/2551</topic><topic>631/337/2019</topic><topic>Antiprotozoal Agents - pharmacology</topic><topic>Antiprotozoal Agents - therapeutic use</topic><topic>Chromosomes</topic><topic>Chromosomes - genetics</topic><topic>Drug Resistance, Microbial - genetics</topic><topic>Gene expression</topic><topic>Genome, Protozoan - genetics</topic><topic>Genomes</topic><topic>Heterogeneity</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Leishmania donovani</topic><topic>Leishmania donovani - genetics</topic><topic>Leishmaniasis, Visceral - drug therapy</topic><topic>Leishmaniasis, Visceral - parasitology</topic><topic>Molecular Sequence Annotation</topic><topic>multidisciplinary</topic><topic>Parasites</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA-Seq</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Splicing</topic><topic>Transcriptome - genetics</topic><topic>Tropism</topic><topic>Vector-borne diseases</topic><topic>Visceral leishmaniasis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Camacho, Esther</creatorcontrib><creatorcontrib>González-de la Fuente, Sandra</creatorcontrib><creatorcontrib>Rastrojo, Alberto</creatorcontrib><creatorcontrib>Peiró-Pastor, Ramón</creatorcontrib><creatorcontrib>Solana, Jose Carlos</creatorcontrib><creatorcontrib>Tabera, Laura</creatorcontrib><creatorcontrib>Gamarro, Francisco</creatorcontrib><creatorcontrib>Carrasco-Ramiro, Fernando</creatorcontrib><creatorcontrib>Requena, Jose M.</creatorcontrib><creatorcontrib>Aguado, Begoña</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Camacho, Esther</au><au>González-de la Fuente, Sandra</au><au>Rastrojo, Alberto</au><au>Peiró-Pastor, Ramón</au><au>Solana, Jose Carlos</au><au>Tabera, Laura</au><au>Gamarro, Francisco</au><au>Carrasco-Ramiro, Fernando</au><au>Requena, Jose M.</au><au>Aguado, Begoña</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2019-04-16</date><risdate>2019</risdate><volume>9</volume><issue>1</issue><spage>6127</spage><epage>6127</epage><pages>6127-6127</pages><artnum>6127</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Leishmania donovani
is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of
L
.
donovani
is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an
L
.
donovani
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 + RNA, 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
cis-
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.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>30992521</pmid><doi>10.1038/s41598-019-42511-4</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-2450-2999</orcidid><orcidid>https://orcid.org/0000-0001-7550-0198</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 2045-2322 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Springer Nature OA Free Journals; Nature Free; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | 38/23 38/39 38/43 38/77 38/91 45 45/90 631/326/417/2551 631/337/2019 Antiprotozoal Agents - pharmacology Antiprotozoal Agents - therapeutic use Chromosomes Chromosomes - genetics Drug Resistance, Microbial - genetics Gene expression Genome, Protozoan - genetics Genomes Heterogeneity Humanities and Social Sciences Humans Leishmania donovani Leishmania donovani - genetics Leishmaniasis, Visceral - drug therapy Leishmaniasis, Visceral - parasitology Molecular Sequence Annotation multidisciplinary Parasites Ribonucleic acid RNA RNA-Seq Science Science (multidisciplinary) Splicing Transcriptome - genetics Tropism Vector-borne diseases Visceral leishmaniasis |
| title | Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation |
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