Genome-wide analysis of alternative splicing in Volvox carteri

Kianianmomeni A, Ong CS, Rätsch G, Hallmann A (2014)
BMC Genomics 15.

Download
OA
Journal Article | Published | English
Author
; ; ;
Abstract
BACKGROUND: Alternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Particularly in multicellular eukaryotes, this mechanism is involved in the regulation of developmental and physiological processes like growth, differentiation and signal transduction. RESULTS: Here we report the genome-wide analysis of alternative splicing in the multicellular green alga Volvox carteri. The bioinformatic analysis of 132,038 expressed sequence tags (ESTs) identified 580 alternative splicing events in a total of 426 genes. The predominant type of alternative splicing in Volvox is intron retention (46.5%) followed by alternative 5[prime] (17.9%) and 3[prime] (21.9%) splice sites and exon skipping (9.5%). Our analysis shows that in Volvox at least ~2.9% of the intron-containing genes are subject to alternative splicing. Considering the total number of sequenced ESTs, the Volvox genome seems to provide more favorable conditions (e.g., regarding length and GC content of introns) for the occurrence of alternative splicing than the genome of its close unicellular relative Chlamydomonas. Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas. Since the Volvox genome contains about the same number of protein-coding genes as the Chlamydomonas genome (~14,500 protein-coding genes), we assumed that alternative splicing may play a key role in generation of genomic diversity, which is required to evolve from a simple one-cell ancestor to a multicellular organism with differentiated cell types [1]. To confirm the alternative splicing events identified by bioinformatic analysis, several genes with different types of alternatively splicing have been selected followed by experimental verification of the predicted splice variants by RT-PCR. CONCLUSIONS: The results show that our approach for prediction of alternative splicing events in Volvox was accurate and reliable. Moreover, quantitative real-time RT-PCR appears to be useful in Volvox for analyses of relationships between the appearance of specific alternative splicing variants and different kinds of physiological, metabolic and developmental processes as well as responses to environmental changes.
Publishing Year
ISSN
Financial disclosure
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
PUB-ID

Cite this

Kianianmomeni A, Ong CS, Rätsch G, Hallmann A. Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics. 2014;15.
Kianianmomeni, A., Ong, C. S., Rätsch, G., & Hallmann, A. (2014). Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics, 15.
Kianianmomeni, A., Ong, C. S., Rätsch, G., and Hallmann, A. (2014). Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics 15.
Kianianmomeni, A., et al., 2014. Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics, 15.
A. Kianianmomeni, et al., “Genome-wide analysis of alternative splicing in Volvox carteri”, BMC Genomics, vol. 15, 2014.
Kianianmomeni, A., Ong, C.S., Rätsch, G., Hallmann, A.: Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics. 15, (2014).
Kianianmomeni, Arash, Ong, Cheng Soon, Rätsch, Gunnar, and Hallmann, Armin. “Genome-wide analysis of alternative splicing in Volvox carteri”. BMC Genomics 15 (2014).
Main File(s)
Access Level
OA Open Access
Last Uploaded
2015-01-27 08:33:30

This data publication is cited in the following publications:
This publication cites the following data publications:

1 Citation in Europe PMC

Data provided by Europe PubMed Central.

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.
Kahles A, Ong CS, Zhong Y, Ratsch G., Bioinformatics 32(12), 2016
PMID: 26873928

62 References

Data provided by Europe PubMed Central.

Origin of the Eumetazoa: testing ecological predictions of molecular clocks against the Proterozoic fossil record.
Peterson KJ, Butterfield NJ, Peterson KJ., Proc. Natl. Acad. Sci. U.S.A. 102(27), 2005
PMID: 15983372
Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.
Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS., Science 329(5988), 2010
PMID: 20616280
The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR., Science 318(5848), 2007
PMID: 17932292
Different levels of alternative splicing among eukaryotes.
Kim E, Magen A, Ast G., Nucleic Acids Res. 35(1), 2007
PMID: 17158149
BLAT--the BLAST-like alignment tool.
Kent WJ., Genome Res. 12(4), 2002
PMID: 11932250
Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.
Ekici OD, Paetzel M, Dalbey RE., Protein Sci. 17(12), 2008
PMID: 18824507
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays.
Moll AG, Lindenmeyer MT, Kretzler M, Nelson PJ, Zimmer R, Cohen CD., PLoS ONE 4(3), 2009
PMID: 19277110
Gene expression profiling of flagellar disassembly in Chlamydomonas reinhardtii.
Chamberlain KL, Miller SH, Keller LR., Genetics 179(1), 2008
PMID: 18493036
Quantitative analysis of cell-type specific gene expression in the green alga Volvox carteri.
Nematollahi G, Kianianmomeni A, Hallmann A., BMC Genomics 7(), 2006
PMID: 17184518
Primary structure and expression of a gamete lytic enzyme in Chlamydomonas reinhardtii: similarity of functional domains to matrix metalloproteases.
Kinoshita T, Fukuzawa H, Shimada T, Saito T, Matsuda Y., Proc. Natl. Acad. Sci. U.S.A. 89(10), 1992
PMID: 1584806

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 25516378
PubMed | Europe PMC

Search this title in

Google Scholar