Fitzpatrick DA

References (2)

Title : Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling - Clarke_2013_Genome.Biol_14_R11
Author(s) : Clarke M , Lohan AJ , Liu B , Lagkouvardos I , Roy S , Zafar N , Bertelli C , Schilde C , Kianianmomeni A , Burglin TR , Frech C , Turcotte B , Kopec KO , Synnott JM , Choo C , Paponov I , Finkler A , Heng Tan CS , Hutchins AP , Weinmeier T , Rattei T , Chu JS , Gimenez G , Irimia M , Rigden DJ , Fitzpatrick DA , Lorenzo-Morales J , Bateman A , Chiu CH , Tang P , Hegemann P , Fromm H , Raoult D , Greub G , Miranda-Saavedra D , Chen N , Nash P , Ginger ML , Horn M , Schaap P , Caler L , Loftus BJ
Ref : Genome Biol , 14 :R11 , 2013
Abstract : BACKGROUND: The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.
RESULTS: Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms.
CONCLUSIONS: Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.
ESTHER : Clarke_2013_Genome.Biol_14_R11
PubMedSearch : Clarke_2013_Genome.Biol_14_R11
PubMedID: 23375108
Gene_locus related to this paper: acaca-l8gel0 , acaca-l8gri8 , acaca-l8h8h3 , acaca-l8gtb6 , acaca-l8gr27 , acaca-l8h9l6 , acaca-l8hhi6 , acaca-l8grd3 , acaca-l8gju3 , acaca-l8h8t7 , acaca-l8h0a7

Title : Evolution of pathogenicity and sexual reproduction in eight Candida genomes - Butler_2009_Nature_459_657
Author(s) : Butler G , Rasmussen MD , Lin MF , Santos MA , Sakthikumar S , Munro CA , Rheinbay E , Grabherr M , Forche A , Reedy JL , Agrafioti I , Arnaud MB , Bates S , Brown AJ , Brunke S , Costanzo MC , Fitzpatrick DA , de Groot PW , Harris D , Hoyer LL , Hube B , Klis FM , Kodira C , Lennard N , Logue ME , Martin R , Neiman AM , Nikolaou E , Quail MA , Quinn J , Santos MC , Schmitzberger FF , Sherlock G , Shah P , Silverstein KA , Skrzypek MS , Soll D , Staggs R , Stansfield I , Stumpf MP , Sudbery PE , Srikantha T , Zeng Q , Berman J , Berriman M , Heitman J , Gow NA , Lorenz MC , Birren BW , Kellis M , Cuomo CA
Ref : Nature , 459 :657 , 2009
Abstract : Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.
ESTHER : Butler_2009_Nature_459_657
PubMedSearch : Butler_2009_Nature_459_657
PubMedID: 19465905
Gene_locus related to this paper: canal-ATG15 , canal-bna7 , canal-c4yl13 , canal-LIP1 , canal-LIP2 , canal-LIP3 , canal-LIP4 , canal-LIP5 , canal-LIP6 , canal-LIP7 , canal-LIP8 , canal-LIP9 , canal-LIP10 , canal-ppme1 , canal-q5a0c9 , canal-q5a2i9 , canal-q5a042 , canal-q5ad17 , canal-q5aeu3 , canal-q5afp8 , canal-q5ag57 , canal-q5ai09 , canal-q5ai12 , canal-q5ajt3 , canal-q5akz5 , canal-q5apu4 , canal-q59l46 , canal-q59m48 , canal-q59nw6 , canal-q59u61 , canal-q59u64 , canal-q59vp0 , canal-q59y97 , canaw-c4ykb1 , canaw-c4yrn6 , canaw-c4yrn9 , canaw-c4yrr3 , canaw-c4yrv3 , canaw-c4ys26 , cantt-c5m3d7 , cantt-c5m3y5 , cantt-c5m4x0 , cantt-c5m5e8 , cantt-c5m5w2 , cantt-c5m8s7 , cantt-c5m9c2 , cantt-c5m465 , cantt-c5m751 , cantt-c5m793 , cantt-c5m893 , cantt-c5ma78 , cantt-c5mag0 , cantt-c5mbb8 , cantt-c5mc53 , cantt-c5md87 , cantt-c5mdy3 , cantt-c5mey7 , cantt-c5mfg0 , cantt-c5mfh8 , cantt-c5mg56 , cantt-c5mgj0 , cantt-c5mh75 , cantt-c5mh80 , cantt-c5mh89 , cantt-c5mhh0 , cantt-c5mhn5 , cantt-c5mij5 , cantt-c5min7 , clal4-c4xvt8 , clal4-c4xwy4 , clal4-c4xy03 , clal4-c4xyx9 , clal4-c4xzz1 , clal4-c4y3e1 , clal4-c4y4f2 , clal4-c4y4w8 , clal4-c4y5j4 , clal4-c4y5j9 , clal4-c4y7z7 , clal4-c4y8q1 , clal4-c4y035 , clal4-c4y481 , clal4-c4y538 , clal4-c4y898 , clal4-c4yas2 , clal4-c4yba6 , clal4-c4yba7 , clal4-c4yc85 , lodel-a5drz3 , lodel-a5ds97 , lodel-a5dsc0 , lodel-a5duu4 , lodel-a5duy7 , lodel-a5dv03 , lodel-a5dv46 , lodel-a5dw16 , lodel-a5dwv7 , lodel-a5dww6 , lodel-a5dxf3 , lodel-a5e0z5 , lodel-a5e1c1 , lodel-a5e1l4 , lodel-a5e1p3 , lodel-a5e2s1 , lodel-a5e2t8 , lodel-a5e2v2 , lodel-a5e4u8 , lodel-a5e5a9 , lodel-a5e5k1 , lodel-a5e5z7 , lodel-a5e6w1 , lodel-a5e028 , lodel-atg15 , lodel-kex1 , picgu-a5d9u2 , picgu-a5dav0 , picgu-a5dbk0 , picgu-a5dc45 , picgu-a5dc73 , picgu-a5dc74 , picgu-a5dc75 , picgu-a5ddt8 , picgu-a5dev7 , picgu-a5dh90 , picgu-a5dhe3 , picgu-a5di38 , picgu-a5dj06 , picgu-a5dkd8 , picgu-a5dle9 , picgu-a5dlj5 , picgu-a5dm19 , picgu-a5dn92 , picgu-a5dnr3 , picgu-a5dnt6 , picgu-a5dqu5 , picgu-a5dr14 , picgu-a5drl3 , picgu-atg15 , picgu-bna7 , picgu-a5d9q3 , picgu-a5dag9 , clal4-c4y5a2 , clal4-c4y0l0 , cantt-c5mcb1 , clal4-c4y8j2 , cantt-c5m494 , clals-a0a202gac7 , canal-hda1 , picgu-a5dks8 , lodel-a5drs6 , canpc-g8bbk1 , cantt-kex1 , clal4-kex1 , picgu-kex1