Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

Biology Direct

Volumn 11, Issue 1, 2016, Pages

  Jakalski, Marcin ^a   Takeshita, Kazutaka ^b,d   Deblieck, Mathieu ^a,e   Koyanagi, Kanako O ^b   Makałowska, Izabela ^c   Watanabe, Hidemi ^b   Makałowski, Wojciech ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b HOKKAIDO UNIVERSITY   (Japan)

^c ADAM MICKIEWICZ UNIVERSITY   (Poland)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^e INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

Author keywords

Chlamydomonas; Comparative genomics; Green algae; Multicellularity; Retrogenes; Retroposition; Volvox

Indexed keywords

ALGAL PROTEIN; PLANT PROTEIN;

CHLAMYDOMONAS REINHARDTII; COMPARATIVE STUDY; GENETICS; METABOLISM; PLANT GENOME; RETROPOSON; VOLVOX;

ALGAL PROTEINS; CHLAMYDOMONAS REINHARDTII; GENOME, PLANT; PLANT PROTEINS; RETROELEMENTS; VOLVOX;

EID: 84984861275     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/s13062-016-0138-1     Document Type: Article

References (61)

1. Nei M. Gene duplication and nucleotide substitution in evolution. Nature. 1969;221:40-2.
2. Ohno S. Evolution by gene duplication. New York: Springer; 1970.
3. Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. 2000;290:1151-5.
4. Long M, Betrán E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nat Rev Genet. 2003;4:865-75.
5. Kaessmann H, Vinckenbosch N, Long M. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet. 2009;10:19-31.
6. Prince VE, Pickett FB. Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet. 2002;3:827-37.
7. Ciomborowska J, Rosikiewicz W, Szklarczyk D, Makalowski W, Makalowska I. "Orphan" retrogenes in the human genome. Mol Bio Evol. 2013;30:384-96.
8. Brosius J. Retroposons--seeds of evolution. Science. 1991;251:753.
9. Kirk DL. Evolution of multicellularity in the volvocine algae. Curr Opin Plant Biol. 1999;2:496-501.
10. Kirk DL. A twelve-step program for evolving multicellularity and a division of labor. Bioessays. 2005;27:299-310.
11. Harris EH. Chlamydomonas as a model organism. Annu Rev Plant Physiol Plant Mol Biol. 2001;52:363-406.
12. Pröschold T, Harris EH, Coleman AW. Portrait of a species: Chlamydomonas reinhardtii. Genetics. 2005;170:1601-10.
13. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007;318:245-50.
14. Herron MD, Hackett JD, Aylward FO, Michod RE. Triassic origin and early radiation of multicellular volvocine algae. Proc Natl Acad Sci U S A. 2009;106:3254-8.
15. Herron MD, Michod RE. Evolution of complexity in the volvocine algae: transitions in individuality through Darwin's eye. Evolution. 2008;62:436-51.
16. Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, et al. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science. 2010;329:223-6.
17. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007;317:86-94.
18. Kabza M, Ciomborowska J, Makałowska I. RetrogeneDB--a database of animal retrogenes. Mol Biol Evol. 2014;31:1646-8.
19. Vinckenbosch N, Dupanloup I, Kaessmann H. Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A. 2006;103:3220-5.
20. Pan D, Zhang L. Burst of young retrogenes and independent retrogene formation in mammals. PLoS One. 2009;4:e5040.
21. Betrán E, Thornton K, Long M. Retroposed new genes out of the X in Drosophila. Genome Res. 2002;12:1854-9.
22. Bai Y, Casola C, Feschotte C, Betrán E. Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol. 2007;8:R11.
23. Du K, He S. Evolutionary fate and implications of retrocopies in the African coelacanth genome. BMC Genomics. 2015;16:915.
24. Navarro FCP, Galante PAF. A genome-wide landscape of retrocopies in primate genomes. Genome Biol Evol. 2015;7:2265-75.
25. Carelli FN, Hayakawa T, Go Y, Imai H, Warnefors M, Kaessmann H. The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res. 2016;26:301-14.
26. Zhang Y, Wu Y, Liu Y, Han B. Computational identification of 69 retroposons in Arabidopsis. Plant Physiol. 2005;138:935-48.
27. Zhu Z, Zhang Y, Long M. Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol. 2009;151:1943-51.
28. Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z, et al. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell. 2006;18:1791-802.
29. Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, et al. Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes. Genome Biol Evol. 2011;3:1357-68.
30. Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, et al. The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell. 2010;22:2943-55.
31. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
32. Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, et al. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 2011;9:e1000602.
33. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell. 1993;72:595-605.
34. Fablet M, Bueno M, Potrzebowski L, Kaessmann H. Evolutionary origin and functions of retrogene introns. Mol Biol Evol. 2009;26:2147-56.
35. Szcześniak MW, Ciomborowska J, Nowak W, Rogozin IB, Makałowska I. Primate and rodent specific intron gains and the origin of retrogenes with splice variants. Mol Biol Evol. 2011;28:33-7.
36. Levasseur A, Pontarotti P. The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics. Biol Direct. 2011;6:11.
37. Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 2010;11:97-108.
38. Zhang J. Evolution by gene duplication: an update. Trends Ecol Evol. 2003;18:292-8.
39. Krasnov AN, Kurshakova MM, Ramensky VE, Mardanov PV, Nabirochkina EN, Georgieva SG. A retrocopy of a gene can functionally displace the source gene in evolution. Nucleic Acids Res. 2005;33:6654-61.
40. Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 2010;20:1313-26.
41. Nematollahi G, Kianianmomeni A, Hallmann A. Quantitative analysis of cell-type specific gene expression in the green alga Volvox carteri. BMC Genomics. 2006;7:321.
42. Merchant SS, Allen MD, Kropat J, Moseley JL, Long JC, Tottey S, et al. Between a rock and a hard place: trace element nutrition in Chlamydomonas. Biochim Biophys Acta. 2006;1763:578-94.
43. Chen H, Romo-Leroux PA, Salin ML. The iron-containing superoxide dismutase-encoding gene from Chlamydomonas reinhardtii obtained by direct and inverse PCR. Gene. 1996;168:113-6.
44. Kianianmomeni A, Ong CS, Rätsch G, Hallmann A. Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics. 2014;15:1117.
45. Phytozome Database. https://phytozome.jgi.doe.gov/pz/portal.html. Last accessed 03 May 2016.
46. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40:D1178-86.
47. Joint Genome Institute (JGI), Chlorella NC64A genome project. http://genome.jgi.doe.gov/ChlNC64A_1/ChlNC64A_1.home.html. Last accessed 12 May 2016.
48. Kang L-F, Zhu Z-L, Zhao Q, Chen L-Y, Zhang Z. Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. BMC Evol Biol. 2012;12:128.
49. Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9:18.
50. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586-91.
51. Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006;34:W609-12.
52. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009;37:D211-5.
53. Pfam2GO dataset. http://geneontology.org/external2go/pfam2go. Last accessed 29 April 2016.
54. McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, et al. AgBase: a functional genomics resource for agriculture. BMC Genomics. 2006;7:229.
55. O'Brien KP, Remm M, Sonnhammer ELL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 2005;33:D476-80.
56. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059-66.
57. Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33:511-8.
58. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688-90.
59. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008;57:758-71.
60. Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree Exploration. BMC Bioinformatics. 2010;11:24.
61. Inkscape Software. https://inkscape.org. Last accessed 12 May 2016.