Opscan ortholog calling, iadhore syntenic fragment from multiple species merged with bedtools
Opscan 0.1, iAdHoRe 3.0.01, Bedtools 2.26
H. glycines synteny with 3 Globodera and 2 Meloidogyne species
April 6, 2018, midnight
Genome structure
This is synteny across all 5 species surveyed and then merged. Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EG, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology 17:124. Abad P, Gouzy J, Aury J-M, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nature biotechnology 26:909. Phillips WS, Howe DK, Brown AM, Eves-Van Den Akker S, Dettwyler L, Peetz AB, Denver DR, Zasada IA (2017) The Draft Genome of Globodera ellingtonae. Journal of nematology 49:127. Opperman CH, Bird DM, Williamson VM, Rokhsar DS, Burke M, Cohn J, Cromer J, Diener S, Gajan J, Graham S, Houfek TD, Liu Q, Mitros T, Schaff J, Schaffer R, Scholl E, Sosinski BR, Thomas VP, Windham E (2008) Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences 105:14802-14807. Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome biology 15:R43.