Novel insights into chromosome evolution in birds, archosaurs, and reptiles

Genome Biology and Evolution

Volumn 8, Issue 8, 2016, Pages 2442-2451

  Farré, Marta ^a   Narayan, Jitendra ^b   Slavov, Gancho T ^b   Damas, Joana ^a   Auvil, Loretta ^c   Li, Cai ^d,e   Jarvis, Erich D ^f,g   Burt, David W ^h   Griffin, Darren K ⁱ   Larkin, Denis M ^a  

^a ROYAL VETERINARY COLLEGE   (United Kingdom)

^b ABERYSTWYTH UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d BGI SHENZHEN   (China)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

^f DUKE UNIVERSITY   (United States)

^g HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^h UNIVERSITY OF EDINBURGH   (United Kingdom)

ⁱ UNIVERSITY OF KENT   (United Kingdom)

Author keywords

Birds; Chromosome rearrangements; Comparative genomics; Genome evolution; Reptiles

Indexed keywords

ANIMAL; BIRD; CHROMOSOMAL MAPPING; CHROMOSOME; CROCODILIAN; DNA SEQUENCE; GENETICS; GENOME; MOLECULAR EVOLUTION; PHYLOGENY; REPTILE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SYNTENY;

ALLIGATORS AND CROCODILES; ANIMALS; BIRDS; CHROMOSOME MAPPING; CHROMOSOMES; EVOLUTION, MOLECULAR; GENOME; PHYLOGENY; REPTILES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; SYNTENY;

EID: 84999103148     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evw166     Document Type: Article

References (44)

1. Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. 2004. Hotspots of mammalian chromosomal evolution. Genome Biol. 5:R23. doi: 10.1186/gb-2004-5-4-r23
2. Bertrand N, Dahmane N. 2006. Sonic hedgehog signaling in forebrain development and its interactions with pathways that modify its effects. Trends Cell Biol. 16:597-605. doi: 10.1016/j.tcb.2006.09.007
3. Brawand D, et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348. doi: 10.1038/nature10532
4. Burt DW, et al. 1999. The dynamics of chromosome evolution in birds and mammals. Nature 402:411-413. doi: 10.1038/46555
5. Chakraborty M, et al. 2015. Core and shell song systems unique to the parrot brain. PLoS One 10:e0118496. doi: 10.1371/ journal.pone.0118496
6. Donthu R, Lewin HA, Larkin DM. 2009. SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence. BMC Res Notes 2:148. doi: 10.1186/1756-0500-2-148
7. Ellegren H. 2010. Evolutionary stasis: the stable chromosomes of birds. Trends Ecol Evol. 25:283-291. doi: 10.1016/j.tree.2009.12.004
8. Elsik CG, Tellam RL, Worley KC. 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-528. doi: 10.1126/science.1169588
9. Grabherr MG, et al. 2010. Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics 26:1145-1151. doi: 10.1093/bioinformatics/btq102
10. Griffin DK, Robertson LB, Tempest HG, Skinner BM. 2007. The evolution of the avian genome as revealed by comparative molecular cytoge-netics. Cytogenet Genome Res. 117:64-77. doi: 10.1159/000103166
11. Groenen MA, et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393-398. doi: 10.1038/nature11622
12. Harrison-Uy SJ, Pleasure SJ. 2012. Wnt signaling and forebrain development. Cold Spring Harb Perspect Biol. 4:a008094. doi: 10.1101/ cshperspect.a008094
13. Hollyday M, McMahon JA, McMahon AP. 1995. Wnt expression patterns in chick embryo nervous system. Mech Dev. 52:9-25.
14. Huang DW, Sherman BT, Lempicki RA. 2008. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44-57. doi: 10.1038/nprot.2008.211
15. Huang Y, et al. 2013. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet. 45:776-783. doi: 10.1038/ng.2657
16. ICGSC. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716. doi: 10.1038/nature03154
17. Islam SM, et al. 2009. Draxin, a repulsive guidance protein for spinal cord and forebrain commissures. Science 323:388-393. doi: 10.1126/ science.1165187
18. Jarvis ED. 2004. Learned birdsong and the neurobiology of human language. Ann N Y Acad Sci. 1016:749-777. doi: 10.1196/ annals.1298.038
19. Jarvis ED, et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331. doi: 10.1126/Science.1253451
20. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 2003. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 100:11484-11489. doi: 10.1073/pnas.1932072100
21. Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921. doi: 10.1038/35057062
22. Larkin DM, et al. 2009. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res. 19:770-777. doi: 10.1101/gr.086546.108
23. Lovell PV, et al. 2014. Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol. 15:565. doi: 10.1186/ s13059-014-0565-1
24. Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV. 2015. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol. 32:23-28. doi: 10.1093/ molbev/msu309
25. Messeguer X, et al. 2002. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics 18:333-334.
26. Murphy WJ, et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613-617. doi: 10.1126/science.1111387
27. Onagbesan OM, et al. 2003. BMPs and BMPRs in chicken ovary and effects of BMP-4 and -7 on granulosa cell proliferation and progesterone production in vitro. Am J Physiol. 285:E973-E983. doi: 10.1152/ ajpendo.00104.2003
28. Pevzner P, Tesler G. 2003. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A. 100:7672-7677. doi: 10.1073/pnas.1330369100
29. Quinlan R, Graf M, Mason I, Lumsden A, Kiecker C. 2009. Complex and dynamic patterns of Wnt pathway gene expression in the developing chick forebrain. Neural Dev. 4:35. doi: 10.1186/ 1749-8104-4-35
30. Rhinn M, Picker A, Brand M. 2006. Global and local mechanisms of forebrain and midbrain patterning. Curr Opin Neurobiol. 16:5-12. doi: 10.1016/j.conb.2006.01.005
31. Robertshaw E, Kiecker C. 2012. Phylogenetic origins of brain organisers. Scientifica (Cairo) 2012:475017. doi: 10.6064/2012/475017
32. Romanov MN, et al. 2014. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 15:1060. doi: 10.1186/1471-2164-15-1060
33. Rouzankina I, Abate-Shen C, Niswander L. 2004. Dlx genes integrate positive and negative signals during feather bud development. Dev Biol. 265:219-233.
34. Ruiz-Herrera A, Farré M, Robinson TJ. 2012. Molecular cytoge-netic and genomic insights into chromosomal evolution. Heredity 108:28-36. doi: 10.1038/hdy.2011.102; 10.1038/ hdy.2011.102
35. Schibler L, et al. 2006. High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution. BMC Genomics 7:194. doi: 10.1186/ 1471-2164-7-
36. Shimogori T, Banuchi V, Ng HY, Strauss JB, Grove EA. 2004. Embryonic signaling centers expressing BMP, WNT and FGF proteins interact to pattern the cerebral cortex. Development 131:5639-5647. doi: 10.1242/dev.01428
37. Suda N, et al. 2014. Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis. Development 141:2885-2894. doi: 10.1242/dev.099150
38. Ullastres A, Farré M, Capilla L, Ruiz-Herrera A. 2014. Unraveling the effect of genomic structural changes in the rhesus macaque-implications for the adaptive role of inversions. BMC Genomics 15:530. doi: 10.1186/1471-2164-15-530
39. Völker M, et al. 2010. Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Res. 20:503-511. doi: 10.1101/ gr.103663.109
40. Wakamatsu Y, Maynard TM, Jones SU, Weston JA. 1999. NUMB localizes in the basal cortex of mitotic avian neuroepithelial cells and modulates neuronal differentiation by binding to NOTCH-1. Neuron 23:71-81.
41. Warren WC, et al. 2010. The genome of a songbird. Nature 464:757-762. doi: 10.1038/nature08819
42. Welten MCM, Verbeek FJ, Meijer AH, Richardson MK. 2005. Gene expression and digit homology in the chicken embryo wing. Evol Dev. 7:18-28. doi: 10.1111/j.1525-142X.2005.05003.x
43. Zeller R, López-Ríos J, Zuniga A. 2009. Vertebrate limb bud development: moving towards integrative analysis of organogenesis. Nat Rev Genet. 10:845-858. doi: 10.1038/nrg2681
44. Zhang G, et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-1320. doi: 10.1126/science.1251385