Difference between revisions of "Using CoGe for the analysis of Plasmodium spp"

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* '''[[GEvo]]''': Microsynteny analysis.
 
* '''[[GEvo]]''': Microsynteny analysis.
 
* '''[[SynMap]]''': Whole genome syntenic analysis.
 
* '''[[SynMap]]''': Whole genome syntenic analysis.
:- '''[[SynMap#Calculating and displaying synonymous/non-synonymous (Ks, Kn), data Kn/Ks Analysis]]''': Characterize the evolution of populations of genes.
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:- '''[[SynMap#Calculating_and_displaying_synonymous.2Fnon-synonymous_.28Ks.2C_Kn.29_data]]''': Characterize the evolution of populations of genes.
 
:- '''[[SPA]]''' tool: Syntenic Path Assembly to assist in genome analysis.
 
:- '''[[SPA]]''' tool: Syntenic Path Assembly to assist in genome analysis.
 
* '''[[SynFind]]''': Identify syntenic genes across multiple genomes.
 
* '''[[SynFind]]''': Identify syntenic genes across multiple genomes.
 
* '''[[CodeOn]]''': Characterize patterns of codon and amino acid evolution in coding sequence.
 
* '''[[CodeOn]]''': Characterize patterns of codon and amino acid evolution in coding sequence.
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<span style="color:#006F00">'''FOLLOW THIS LINK FOR A QUICK OVERVIEW OF [[Plasmodia comparative genomics]] WITH COGE.'''</span>
  
  
 
=='''A brief introduction to ''Plasmodium'' genome evolution'''==
 
=='''A brief introduction to ''Plasmodium'' genome evolution'''==
  
The study of parasitic genomes via comparative genomics offers many unique challenges. Parasite genomes are characterized by a combination of gene loss and the acquisition of species- or lineage-specific genes; in particular, many specialized genes mediate host–parasite interaction <ref>Jackson AP. 2015. Preface. The evolution of parasite genomes and the origins of parasitism. Parasitology. 142 Suppl 1:S1-5. https://www.ncbi.nlm.nih.gov/pubmed/25656359</ref>. The dynamic nature of parasitic genomes is particularly evident within the genus ''Plasmodium''. The genus emerged ~40 million years ago and harbors roughly 200 species of parasitic protozoa better known as malaria parasites. All ''Plasmodium'' species have a complex life cycle involving some kind of vertebrate host and a mosquito vector of the genus ''Anopheles'' (mammals) or ''Culex'' (birds). In addition, ''Plasmodium'' species share similar life cycle characteristics, albeit with a few exceptions (''e.g.'' hypnozoites). However, host and vector preferences differ among ''Plasmodium'' species <ref>Sinka ME, Bangs MJ, Manguin S, Rubio-Palis Y, Chareonviriyaphap T, Coetzee M, Mbogo CM, Hemingway J, Patil AP, Temperley WH, Gething PW, Kabaria CW, Burkot TR, Harbach RE, Hay SI. 2012. A global map of dominant malaria vectors. Parasit Vectors. 5:69. https://www.ncbi.nlm.nih.gov/pubmed/22475528</ref>.
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The genus ''Plasmodium'' emerged ~40 million years ago and harbors roughly 200 species of parasitic protozoa better known as malaria parasites. All ''Plasmodium'' species have a complex life cycle involving some kind of vertebrate host and a mosquito vector. In addition, ''Plasmodium'' species share similar life cycle characteristics, albeit with a few exceptions (''e.g.'' hypnozoites). ''Plasmodium'' genomes are tiny (between 17-28Mb) in comparison to those of their vertebrate (1Gb for birds; 2-3Gb for mammals) and mosquito (230–284Mbp) hosts <ref>DeBarry JD, Kissinger JC. 2011. Jumbled Genomes: Missing Apicomplexan Synteny. Mol Biol Evol. 2011 Oct; 28(10): 2855–2871. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176833/</ref>. All ''Plasmodium'' genomes consist of fourteen chromosomes (nuclear genome), as well as a mitochondrial and apicoplast genome. Despite these shared genomic characteristics, the structural organization, gene content, and sequence of ''Plasmodium'' genomes is highly variably within the genus <ref>Carlton JM, Perkins SL, Deitsch KW. 2013. '''''Malaria Parasites'''''. Caister Academic Press</ref>. The exact origins and mechanisms of these differences remain largely unexplored, however, they are generally hypothesized to stem from host shift events <ref>Prugnolle F, Durand P, Ollomo B, Duval L, Ariey F, Arnathau C, Gonzalez JP, Leroy E, Renaud F. 2011. A Fresh Look at the Origin of Plasmodium falciparum, the Most Malignant Malaria Agent. PLoS Pathog. 7: e1001283. http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1001283</ref><ref>Prugnolle F, Rougeron V, Becquart P, Berry A, Makanga B, Rahola N, Arnathau C, Ngoubangoye B, Menard S, Willaume E, Ayala FJ, Fontenille D, Ollomo B, Durand P, Paupy C, Renaud F. 2013. Diversity, host switching and evolution of Plasmodium vivax infecting African great apes. Proc Natl Acad Sci U S A. 110:8123-8. https://www.ncbi.nlm.nih.gov/pubmed/23637341</ref>.
 
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''Plasmodium'' genomes are tiny (between 17-28Mb) in comparison to those of their vertebrate (1Gb for birds; 2-3Gb for mammals) and mosquito (230–284Mbp) hosts <ref>DeBarry JD, Kissinger JC. 2011. Jumbled Genomes: Missing Apicomplexan Synteny. Mol Biol Evol. 2011 Oct; 28(10): 2855–2871. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176833/</ref>. All ''Plasmodium'' genomes consist of fourteen chromosomes (nuclear genome), as well as a mitochondrial and apicoplast genome. Despite these shared genomic characteristics, the structural organization, gene content, and sequence of ''Plasmodium'' genomes is highly variably within the genus <ref>Carlton JM, Perkins SL, Deitsch KW. 2013. '''''Malaria Parasites'''''. Caister Academic Press</ref>. The exact origins and mechanisms of these differences remain largely unexplored, however, they are generally hypothesized to stem from host shift events <ref>Prugnolle F, Durand P, Ollomo B, Duval L, Ariey F, Arnathau C, Gonzalez JP, Leroy E, Renaud F. 2011. A Fresh Look at the Origin of Plasmodium falciparum, the Most Malignant Malaria Agent. PLoS Pathog. 7: e1001283. http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1001283</ref><ref>Prugnolle F, Rougeron V, Becquart P, Berry A, Makanga B, Rahola N, Arnathau C, Ngoubangoye B, Menard S, Willaume E, Ayala FJ, Fontenille D, Ollomo B, Durand P, Paupy C, Renaud F. 2013. Diversity, host switching and evolution of Plasmodium vivax infecting African great apes. Proc Natl Acad Sci U S A. 110:8123-8. https://www.ncbi.nlm.nih.gov/pubmed/23637341</ref>.
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An increase in funding devoted to malaria research has coincided with a dramatic increase in publicly available genomic information for ''Plasmodium'' <ref>Buscaglia CA, Kissinger JC, Agüero F. 2015. Neglected Tropical Diseases in the Post-Genomic Era. Trends Genet. 31:539-55. https://www.ncbi.nlm.nih.gov/pubmed/26450337</ref>. The most prominent repository is found at NCBI/Genbank <ref>Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2016. GenBank. Nucleic Acids Res. 44: D67–D72. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702903/</ref>; while additional and unique sequences can also be found on other databases:  [http://plasmodb.org/plasmo/ PlasmoDB] <ref>Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H. 2009. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 37:D539-43. https://www.ncbi.nlm.nih.gov/pubmed/18957442</ref>, [http://www.genedb.org/Homepage GeneDB] <ref>Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G, McQuillan JA, Carver T, Aslett M, Olsen C, Subramanian S, Phan I, Farris C, Mitra S, Ramasamy G, Wang H, Tivey A, Jackson A, Houston R, Parkhill J, Holden M, Harb OS, Brunk BP, Myler PJ, Roos D, Carrington M, Smith DF, Hertz-Fowler C, Berriman M. 2012. GeneDB--an annotation database for pathogens. Nucleic Acids Res. 40:D98-108. https://www.ncbi.nlm.nih.gov/pubmed/22116062</ref>, and [http://mbio-serv2.mbioekol.lu.se/Malavi/ MalAvi] <ref>Bensch S, Hellgren O, Pérez-Tris J. 2009. MalAvi: a public database of malaria parasites and related haemosporidian in avian hosts based on mitochondrial cytochrome b lineages. Mol Ecol Resour. 9:1353-8. https://www.ncbi.nlm.nih.gov/pubmed/21564906</ref>. This wealth of genomic data facilitates detailed comparative genomic approaches, opening the possibility to:  
 
An increase in funding devoted to malaria research has coincided with a dramatic increase in publicly available genomic information for ''Plasmodium'' <ref>Buscaglia CA, Kissinger JC, Agüero F. 2015. Neglected Tropical Diseases in the Post-Genomic Era. Trends Genet. 31:539-55. https://www.ncbi.nlm.nih.gov/pubmed/26450337</ref>. The most prominent repository is found at NCBI/Genbank <ref>Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2016. GenBank. Nucleic Acids Res. 44: D67–D72. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702903/</ref>; while additional and unique sequences can also be found on other databases:  [http://plasmodb.org/plasmo/ PlasmoDB] <ref>Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H. 2009. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 37:D539-43. https://www.ncbi.nlm.nih.gov/pubmed/18957442</ref>, [http://www.genedb.org/Homepage GeneDB] <ref>Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G, McQuillan JA, Carver T, Aslett M, Olsen C, Subramanian S, Phan I, Farris C, Mitra S, Ramasamy G, Wang H, Tivey A, Jackson A, Houston R, Parkhill J, Holden M, Harb OS, Brunk BP, Myler PJ, Roos D, Carrington M, Smith DF, Hertz-Fowler C, Berriman M. 2012. GeneDB--an annotation database for pathogens. Nucleic Acids Res. 40:D98-108. https://www.ncbi.nlm.nih.gov/pubmed/22116062</ref>, and [http://mbio-serv2.mbioekol.lu.se/Malavi/ MalAvi] <ref>Bensch S, Hellgren O, Pérez-Tris J. 2009. MalAvi: a public database of malaria parasites and related haemosporidian in avian hosts based on mitochondrial cytochrome b lineages. Mol Ecol Resour. 9:1353-8. https://www.ncbi.nlm.nih.gov/pubmed/21564906</ref>. This wealth of genomic data facilitates detailed comparative genomic approaches, opening the possibility to:  
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* Identify the potential historical interactions that might have lead to the development of genomic adaptations.
 
* Identify the potential historical interactions that might have lead to the development of genomic adaptations.
  
Through a case study on  ''Plasmodium'' evolution, we will illustrate how CoGe can be used for the analysis of multigene families, local synteny, and whole genome comparisons (genome composition, rearrangement events, and gene order conservation).
 
  
 
== '''Finding and integrating Plasmodium genomes in CoGe ''' ==
 
== '''Finding and integrating Plasmodium genomes in CoGe ''' ==
  
You can find the details of Plasmodium genome integration in the following link: [[Finding and intregating Plasmodium genomes to CoGe]]
+
You can find the details of ''Plasmodium'' spp. genome integration in the following link: [[Finding and intregating Plasmodium genomes to CoGe]]
  
  
=='''Using CoGe tools to perform comparative analyses'''==
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=='''Comparative analyses workflows'''==
  
==='''Workflows'''===
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The following links direct to specific tools for the comparative analysis of ''Plasmodium'' genomes:
 
+
The following links direct to specific tools for the comparative analysis of Plasmodium genomes:
+
  
 
[[Plasmodium analysis workflow 1: Tools that evaluate genomic properties and amino acid usage]]
 
[[Plasmodium analysis workflow 1: Tools that evaluate genomic properties and amino acid usage]]
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[[Plasmodium analysis workflow 3: Tools useful on the study of multigene families]]
 
[[Plasmodium analysis workflow 3: Tools useful on the study of multigene families]]
  
=== ''Additional tools for genome analysis with CoGe'' ===
 
 
You can learn about the SPA usage on ''Plasmodium genomes'' in the following link: [[Plasmodium genome analysis using Syntenic Path Assembly]]
 
  
 
=='''Overall conclusions'''==
 
=='''Overall conclusions'''==
  
The number of available ''Plasmodium'' genomes has increased considerably during recent years. This wealth of genomic information creates an unprecedented opportunity to study the unique genomic qualities of this genus using comparative genomics.
+
Insights into the unique patterns of ''Plasmodium'' biology, epidemiology, ecology, and genetics can be obtained from molecular and comparative genomic studies. The rapid growth of genomic information makes implementing tools that facilitate assessing genome evolutionary trends an imperative task. The services and tools provided by the CoGe platform are of considerable use in advancing ''Plasmodium'' comparative genomics. Here, we showed how various CoGe tools could be used to assess evolutionary patterns unique to ''Plasmodium''. We also showed how to use this platform to further characterize sequenced ''Plasmodium'' genomes. Overall, we have demonstrated that CoGe’s tools can be used to address evolutionary questions such as:  
 
+
There have been tremendous achievements in malaria treatment and control strategies. Thanks to worldwide efforts, there has been a significant reduction in the number of malaria cases and malaria-related deaths between 2000 and 2015. By 2015, it was estimated that the number of malaria cases decreased from 262 million to 214 million, and the number of malaria-related deaths from 839,000 to 438,000 <ref>World Health Organization. (2015). World Malaria Report 2015. Retrieved from http://www.who.int/malaria/publications/world-malaria-report-2015/report/en/</ref>.  However, there are still numerous aspects of malaria research that need to be further addressed. 
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The intricacies of parasite-host relations in ''Plasmodium'' infection might be more complex than previously considered <ref>Garamszegi LZ. 2009. Patterns of co-speciation and host switching in primate malaria parasites. Malar J. 110. doi: 10.1186/1475-2875-8-110. https://www.ncbi.nlm.nih.gov/pubmed/19463162</ref>. Humans have recently been infected by ''Plasmodium'' species classically considered specific to non-human primates (''e.g.'' a single infection with ''P. cynomolgi'' <ref>Ta TH, Hisam S, Lanza M, Jiram AI, Ismail N, Rubio JM. 2014. First case of a naturally acquired human infection with ''Plasmodium cynomolgi''. Malar J. 13: 68. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937822/</ref> and various infections with ''P. knowlesi'' <ref>Singh B, Daneshvar C. 2013. Human infections and detection of Plasmodium knowlesi. Clin Microbiol Rev. 26:165-84.  https://www.ncbi.nlm.nih.gov/pubmed/23554413</ref>). In addition, african primates have been infected by unique ''P. falciparum'' strains (a parasite classically considered exclusive to humans) and are proposed to act as reservoirs for this parasite <ref>Prugnolle F, Durand P, Neel C, Ollomo B, Ayala FJ, Arnathau C, Etienne L, Mpoudi-Ngole E, Nkoghe D, Leroy E, Delaporte E, Peeters M, Renaud F. 2010. African great apes are natural hosts of multiple related malaria species, including ''Plasmodium falciparum''. Proc Natl Acad Sci U S A. 107:1458-63. https://www.ncbi.nlm.nih.gov/pubmed/20133889</ref><ref>Duval L, Fourment M, Nerrienet E, Rousset D, Sadeuh SA, Goodman SM, Andriaholinirina NV, Randrianarivelojosia M, Paul RE, Robert V, Ayala FJ, Ariey F. 2010. African apes as reservoirs of ''Plasmodium falciparum'' and the origin and diversification of the ''Laverania'' subgenus. Proc Natl Acad Sci U S A. 107:10561-6. https://www.ncbi.nlm.nih.gov/pubmed/20498054</ref>. In bird ''Plasmodium'', the putative evolutionary time of parasite-host associations has a significant role in the development of pathogenicity and in host mortality <ref>Krizanauskiene A, Hellgren O, Kosarev V, Sokolov L, Bensch S, Valkiunas G. 2006. Variation in host specificity between species of avian haemosporidian parasites: evidence from parasite morphology and cytochrome B gene sequences. J Parasitol. 6:1319-24. https://www.ncbi.nlm.nih.gov/pubmed/17304814</ref>. Finally, multiple host-switch events between largely divergent host types are thought to have occurred in bat ''Haemosporidia'' <ref>Duval L, Robert V, Csorba G, Hassanin A, Randrianarivelojosia M, Walston J, Nhim T, Goodman SM, Ariey F. 2007. Multiple host-switching of Haemosporidia parasites in bats. Malar J. 6:157. https://www.ncbi.nlm.nih.gov/pubmed/18045505</ref>. These cases highlight the complexity of the ''Plasmodium'' infection landscape. Insights into the unique patterns of ''Plasmodium'' biology, epidemiology, ecology, and genetics can be obtained from molecular and comparative genomic studies.  
+
 
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The rapid growth of genomic information makes implementing tools that facilitate assessing genome evolutionary trends an imperative task. The services and tools provided by the CoGe platform are of considerable use in advancing ''Plasmodium'' comparative genomics. Here, we showed how various CoGe tools could be used to assess evolutionary patterns unique to ''Plasmodium''. We also showed how to use this platform to further characterize sequenced ''Plasmodium'' genomes. Overall, we have demonstrated that CoGe’s tools can be used to address evolutionary questions such as:  
+
 
*The evolutionary origins of ''Laveranian'' AT-rich genomes.  
 
*The evolutionary origins of ''Laveranian'' AT-rich genomes.  
 
*The location and nature of genome rearrangements between ''Plasmodium''.
 
*The location and nature of genome rearrangements between ''Plasmodium''.

Latest revision as of 13:29, 14 February 2017

About this guide

This 'cookbook' style document is meant to provide an introduction to many of our tools and services and is structured around a case study of investigating genome evolution of the malaria-causing Plasmodium spp. The small size and unique features of this pathogen's genome make it ideal for beginning to understand how our tools can be used to conduct comparative genomic analyses and uncover meaningful discoveries.

Through a number of example analyses, this guide will teach users about the following tools:

  • LoadGenome: Add a new genome to CoGe.
  • LoadAnnotation: Add structural and/or functional annotations to a genome.
  • GenomeInfo: Get information about a genome.
  • GenomeList: Get information about several genomes in a table.
  • CoGeBLAST: BLAST against any set of genomes.
  • GEvo: Microsynteny analysis.
  • SynMap: Whole genome syntenic analysis.
- SynMap#Calculating_and_displaying_synonymous.2Fnon-synonymous_.28Ks.2C_Kn.29_data: Characterize the evolution of populations of genes.
- SPA tool: Syntenic Path Assembly to assist in genome analysis.
  • SynFind: Identify syntenic genes across multiple genomes.
  • CodeOn: Characterize patterns of codon and amino acid evolution in coding sequence.


FOLLOW THIS LINK FOR A QUICK OVERVIEW OF Plasmodia comparative genomics WITH COGE.


A brief introduction to Plasmodium genome evolution

The genus Plasmodium emerged ~40 million years ago and harbors roughly 200 species of parasitic protozoa better known as malaria parasites. All Plasmodium species have a complex life cycle involving some kind of vertebrate host and a mosquito vector. In addition, Plasmodium species share similar life cycle characteristics, albeit with a few exceptions (e.g. hypnozoites). Plasmodium genomes are tiny (between 17-28Mb) in comparison to those of their vertebrate (1Gb for birds; 2-3Gb for mammals) and mosquito (230–284Mbp) hosts [1]. All Plasmodium genomes consist of fourteen chromosomes (nuclear genome), as well as a mitochondrial and apicoplast genome. Despite these shared genomic characteristics, the structural organization, gene content, and sequence of Plasmodium genomes is highly variably within the genus [2]. The exact origins and mechanisms of these differences remain largely unexplored, however, they are generally hypothesized to stem from host shift events [3][4].

An increase in funding devoted to malaria research has coincided with a dramatic increase in publicly available genomic information for Plasmodium [5]. The most prominent repository is found at NCBI/Genbank [6]; while additional and unique sequences can also be found on other databases: PlasmoDB [7], GeneDB [8], and MalAvi [9]. This wealth of genomic data facilitates detailed comparative genomic approaches, opening the possibility to:

  • Infer origins of certain traits, specialized phenotypes, and genomic features.
  • Track the maintenance of conserved genes across the genus, as well as the gain or loss of genes unique to a single species or a group of closely related species.
  • Identify the potential historical interactions that might have lead to the development of genomic adaptations.


Finding and integrating Plasmodium genomes in CoGe

You can find the details of Plasmodium spp. genome integration in the following link: Finding and intregating Plasmodium genomes to CoGe


Comparative analyses workflows

The following links direct to specific tools for the comparative analysis of Plasmodium genomes:

Plasmodium analysis workflow 1: Tools that evaluate genomic properties and amino acid usage

Plasmodium analysis workflow 2: Tools for the syntenic analysis of whole genomes and microsyntenic regions

Plasmodium analysis workflow 3: Tools useful on the study of multigene families


Overall conclusions

Insights into the unique patterns of Plasmodium biology, epidemiology, ecology, and genetics can be obtained from molecular and comparative genomic studies. The rapid growth of genomic information makes implementing tools that facilitate assessing genome evolutionary trends an imperative task. The services and tools provided by the CoGe platform are of considerable use in advancing Plasmodium comparative genomics. Here, we showed how various CoGe tools could be used to assess evolutionary patterns unique to Plasmodium. We also showed how to use this platform to further characterize sequenced Plasmodium genomes. Overall, we have demonstrated that CoGe’s tools can be used to address evolutionary questions such as:

  • The evolutionary origins of Laveranian AT-rich genomes.
  • The location and nature of genome rearrangements between Plasmodium.
  • The evolutionary patterns of genes crucial in cell invasion.
  • The evolutionary trends of multigene families.


Useful links

Plasmodium Notebooks in CoGe

Link to Notebook for published Plasmodium genome data: https://genomevolution.org/coge/NotebookView.pl?lid=1753
Link to Notebook for published P. falciparum strains: https://genomevolution.org/coge/NotebookView.pl?lid=1758
Link to Notebook for published P. vivax strains: https://genomevolution.org/coge/NotebookView.pl?lid=1760
Link to Notebook for published Plasmodium apicoplast data: https://genomevolution.org/coge/NotebookView.pl?lid=1754
Link to Notebook for published Plasmodium mitochondrion data: https://genomevolution.org/coge/NotebookView.pl?lid=1756

Sample data

  • Gene sequences used on CoGeBLAST analysis (obtained from PlasmoDB):
PVX_113230.1 | Plasmodium vivax Sal-1 | variable surface protein Vir14-related (http://plasmodb.org/plasmo/app/record/gene/PVX_113230)
PVX_096004.1 | Plasmodium vivax Sal-1 | VIR protein (http://plasmodb.org/plasmo/app/record/gene/PVX_096004)
  • Gene sequence used on SynFind to inform GEvo analysis (obtained from PlasmoDB):
PVX_003830.1 | Plasmodium vivax Sal-1 | serine-repeat antigen 5 (SERA) (http://plasmodb.org/plasmo/app/record/gene/PVX_003830)
  • Gene sequences used on CoGeBLAST to inform GEvo analysis (obtained from PlasmoDB):
PF3D7_0424100.1 | Plasmodium falciparum 3D7 | reticulocyte binding protein homologue 5 (http://plasmodb.org/plasmo/app/record/gene/PF3D7_0424100)
PVX_096410.1 | Plasmodium vivax Sal-1 | cysteine repeat modular protein 2, putative (http://plasmodb.org/plasmo/app/record/gene/PVX_096410)


References

  1. DeBarry JD, Kissinger JC. 2011. Jumbled Genomes: Missing Apicomplexan Synteny. Mol Biol Evol. 2011 Oct; 28(10): 2855–2871. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176833/
  2. Carlton JM, Perkins SL, Deitsch KW. 2013. Malaria Parasites. Caister Academic Press
  3. Prugnolle F, Durand P, Ollomo B, Duval L, Ariey F, Arnathau C, Gonzalez JP, Leroy E, Renaud F. 2011. A Fresh Look at the Origin of Plasmodium falciparum, the Most Malignant Malaria Agent. PLoS Pathog. 7: e1001283. http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1001283
  4. Prugnolle F, Rougeron V, Becquart P, Berry A, Makanga B, Rahola N, Arnathau C, Ngoubangoye B, Menard S, Willaume E, Ayala FJ, Fontenille D, Ollomo B, Durand P, Paupy C, Renaud F. 2013. Diversity, host switching and evolution of Plasmodium vivax infecting African great apes. Proc Natl Acad Sci U S A. 110:8123-8. https://www.ncbi.nlm.nih.gov/pubmed/23637341
  5. Buscaglia CA, Kissinger JC, Agüero F. 2015. Neglected Tropical Diseases in the Post-Genomic Era. Trends Genet. 31:539-55. https://www.ncbi.nlm.nih.gov/pubmed/26450337
  6. Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2016. GenBank. Nucleic Acids Res. 44: D67–D72. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702903/
  7. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H. 2009. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 37:D539-43. https://www.ncbi.nlm.nih.gov/pubmed/18957442
  8. Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G, McQuillan JA, Carver T, Aslett M, Olsen C, Subramanian S, Phan I, Farris C, Mitra S, Ramasamy G, Wang H, Tivey A, Jackson A, Houston R, Parkhill J, Holden M, Harb OS, Brunk BP, Myler PJ, Roos D, Carrington M, Smith DF, Hertz-Fowler C, Berriman M. 2012. GeneDB--an annotation database for pathogens. Nucleic Acids Res. 40:D98-108. https://www.ncbi.nlm.nih.gov/pubmed/22116062
  9. Bensch S, Hellgren O, Pérez-Tris J. 2009. MalAvi: a public database of malaria parasites and related haemosporidian in avian hosts based on mitochondrial cytochrome b lineages. Mol Ecol Resour. 9:1353-8. https://www.ncbi.nlm.nih.gov/pubmed/21564906