Vertebrate Genome Evolution

Vertebrate Genome Evolution

The overarching theme of my research is vertebrate genome evolution, particularly with respect to the effects of gene and genome duplication on genome composition and gene regulation. Most of my research has focused on homeobox genes of the Hox and ParaHox gene families and especially the Pancreas and duodenal homoebox genes (Pdx1 and Pdx2). Past models for this research have included Actinopterygian (ray-finned) fish such as zebrafish, gars, bowfin and Polypterus, “living fossils” such as lungfish and coelacanths and cartilaginous fish including the Little skate (Leucoraja erinacea) and Lesser spotted catshark (Scyliorhinus canicula). More recently I’ve turned to Mongolian gerbils (Meriones unguiculatus) as an interesting and informative new model of vertebrate genome evolution.

Mongolian gerbils

Fat sandrat   Spotted gar   Spotted gar embryo

Relevant publications:

Pracana, R., Hargreaves, AD., Mulley, JF., Holland, PWH. (2020) ‘Runaway GC evolution in gerbil genomes.’ Molecular Biology and Evolution (in press) [Link]

Mulley, JF (2019) ‘Greater loss of female embryos during human pregnancy: A novel mechanism.’ BioEssays 41, 1900063 [Link] [Preprint]

Brekke, TD., Supriya, S., Denver, MG., Thom, A., Mulley JF. (2019) ‘A high-density genetic map and molecular sex-typing assay for gerbils’ Mammalian Genome 30 (3-4): 63-70 [Link] [Preprint]

Brekke, TD., Steele, KS., and Mulley, JF. (2018) ‘Inbred or Outbred? Genetic diversity in laboratory rodent colonies’ G3: Genes, Genomes, Genetics 8: 679-686 [Link] [Preprint]

Hargreaves, AD, Zhou, L., Christensen, J., Marletaz, F., Liu, S., Jansen, PD., Spiga, E., Hansen, MT., Pedersen, SVH., Biswas, S., Serikawa, K., Fox, BA., Taylor, WR., Mulley, JF., Zhang, G., Heller, RS., Holland, PWH. (2016) ‘Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster’ PNAS 114 (29): 7677–7682

Braasch, I, Gehrke, AR, Smith, JJ, Kawasaki, K, Manousaki, T, Pasquier, J, Amores, A, Desvignes, T, Batzel, P, Catchen, J, Berlin, AM, Campbell, MS, Barrell, D, Martin, KJ, Mulley, JF, Ravi, V, Lee, AP, Nakamura, T, Chalopin, D, Fan, S, Wcisel, D, Cañestro, C, Sydes, J, Beaudry, FEG, Sun, Y, Hertel, J, Beam, MJ, Fasold, M, Ishiyama, M, Johnson, J, Kehr, S, Lara, M, Letaw, JH, Litman, W, Litman, RT, Mikami, M, Ota, T, Saha, NR, Williams, L, Stadler, PF, Wang, H, Taylor, JS, Fontenot, Q, Ferrara, A, Searle, SMJ, Aken, B, Yandell, M, Schneider, I, Yoder, JA, Volff, J-N, Meyer, A, Amemiya, CT, Venkatesh, B, Holland, PWH, Guiguen, Y, Bobe, J, Shubin, NH, Di Palma, F, Alföldi, J, Lindblad-Toh, K, Postlethwait, JH (2016) ‘The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons’ Nature Genetics 48: 427-437

Mulley JF, Hargreaves AD, Hegarty MJ, Heller RS, Swain MT (2014) ‘Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function’ BMC Genomics 15: 1074

Hargreaves AD, Swain MT, Logan DW and Mulley JF (2014) ‘Testing the Toxicofera: comparative reptile transcriptomics casts doubt on the single, early evolution of the reptile venom system’ Toxicon 92: 140-156

Hargreaves AD, Swain MT, Hegarty MJ, Logan DW and Mulley JF (2014) ‘Restriction and recruitment – gene duplication and the origin and evolution of snake venom toxins’ Genome Biology and Evolution 6(8): 2088-2095  

Mulley, JF & Holland, PWH (2014) “Genomic organisation of the seven ParaHox genes of coelacanths.” Journal of Experimental Zoology B: Molecular and Developmental Evolution(Coelacanth genome companion issue) 322B: 352-358

Mulley, JF & Holland, PWH (2010) “Parallel retention of Pdx2 genes in cartilaginous fish and coelacanths.” Molecular Biology and Evolution 27: 2386

Mulley, JF, Zhong, Y-F. & Holland, PWH (2009) “Comparative genomics of Chondrichthyan hoxa clusters.” BMC Evolutionary Biology 9: 218

Furlong, RF & Mulley, JF (2008) “ParaHox Cluster Evolution – Hagfish and Beyond.” Zoological Science 25: 955

Mulley, JF, Chiu, C-H & Holland, PWH (2006) “Break-up of a homeobox gene cluster after genome duplication in teleosts.” PNAS 103: 10369

Mulley, J & Holland P (2004) “Small genome, big insights.” Nature 431: 916