View source for Using CoGe for the analysis of Plasmodium spp

=='''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.


<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'''==

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>.

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: 
* 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'''==
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