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i5k Workspace@NAL
U.S. Department of Agriculture

JAMg Consensus Gene Set v1

Summary
Summary
Resource Type
Genome Annotation
Name
JAMg Consensus Gene Set v1
Program, Pipeline, Workflow or Method Name
JAMg
Program Version
NA
Data Source
Source Name
: Ceratitis capitata whole genome assembly, NCBI release
Organism
C. capitata (Mediterranean fruit fly)
Publication
Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castañera P, Cavanaugh JP, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, González-Guzmán M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernández-Crespo P, Hughes DS, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Munoz-Torres , Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu J, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Ureña E, Vlachos IS, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM. The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species.. Genome biology. 2016 09 22; 17(1):192.
Description

Consensus gene set generated by Alexie Papanicolaou and Just_Annotated_My_genome – using 3 publicly available RNA-Seq libraries and several private ones (gut and reproductive tissues of adults) from Oberhofer. Method is based on i) de-novo predictions with Augustus, Glimmer, SNAP, GeneMark, ii) RNA-Seq using Trinity RNASeq de-novo and Trinity Genome Guided, iii) PASA2 RNASeq integration and iv) Evidence Modeller. Full method available on http://jamg.sourceforge.net(link is external)