Imprecise intron losses are less frequent than precise intron losses but are not rare in plants

Biology Direct

Deng-Ke Niu³  Yu-Fei Yang¹  Heng-Yuan Liu³  Xin-Ran Lan³  Xue-Nan Li²  Tao Zhu³  Ming-Yue Ma³ 

[1]Present address: Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

[2]Beijing Computing Center, Beijing 10094, China

[3]MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China

关键词: Arabidopsis thaliana;    Solanum;    Deletion;    Insertion;    De-exonization;    De-intronization;    Intron loss;   

Others  :  1206329
DOI  :  10.1186/s13062-015-0056-7

 received in 2015-02-12, accepted in 2015-04-24,  发布年份 2015

【 摘 要 】

In this study, we identified 19 intron losses, including 11 precise intron losses (PILs), six imprecise intron losses (IILs), one de-exonization, and one exon deletion in tomato and potato, and 17 IILs in Arabidopsis thaliana. Comparative analysis of related genomes confirmed that all of the IILs have been fixed during evolution. Consistent with previous studies, our results indicate that PILs are a major type of intron loss. However, at least in plants, IILs are unlikely to be as rare as previously reported.

【 授权许可】

   
2015 Ma et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Llopart A, Comeron JM, Brunet FG, Lachaise D, Long M: Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc Natl Acad Sci U S A 2002, 99(12):8121-6.
• [2]Loh Y-H, Brenner S, Venkatesh B: Investigation of loss and gain of introns in the compact genomes of Pufferfishes (Fugu and Tetraodon). Mol Biol Evol 2008, 25(3):526-35.
• [3]Zhu T, Niu DK: Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss. BMC Biol 2013, 11(1):23. BioMed Central Full Text
• [4]Zhu T, Niu DK: Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces. PLoS One 2013, 8(4):e61683.
• [5]Kent WJ, Zahler AM: Conservation, regulation, synteny, and introns in a large-scale C-briggsae-C-elegans genomic alignment. Genome Res 2000, 10(8):1115-25.
• [6]Coulombe-Huntington J, Majewski J: Intron loss and gain in Drosophila. Mol Biol Evol 2007, 24(12):2842-50.
• [7]Farlow A, Meduri E, Dolezal M, Hua L, Schlotterer C: Nonsense-mediated decay enables intron gain in Drosophila. PLoS Genet 2010, 6(1):e1000819.
• [8]Roy SW, Penny D: Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res 2006, 16(10):1270-5.
• [9]Roy SW, Penny D: Patterns of intron loss and gain in plants: Intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol 2007, 24(1):171-81.
• [10]Roy SW, Penny D: Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. Mol Biol Evol 2007, 24(9):1926-33.
• [11]Roy SW, Hartl DL: Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number. Genome Res 2006, 16(6):750-6.
• [12]Da Lage JL, Binder M, Hua-Van A, Janecek S, Casane D: Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial alpha-amylase gene to Basidiomycetes. BMC Evol Biol 2013, 13:40. BioMed Central Full Text
• [13]Mitrovich QM, Tuch BB, De La Vega FM, Guthrie C, Johnson AD: Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss. Science 2010, 330(6005):838-41.
• [14]Irimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, Roy SW: Origin of introns by ‘intronization’ of exonic sequences. Trends Genet 2008, 24(8):378-81.
• [15]Yenerall P, Krupa B, Zhou L: Mechanisms of intron gain and loss in Drosophila. BMC Evol Biol 2011, 11(1):364. BioMed Central Full Text
• [16]Fink GR: Pseudogenes in yeast? Cell 1987, 49(1):5-6.
• [17]The Tomato Genome Consortium: The tomato genome sequence provides insights into fleshy fruit evolution Nature 2012, 485(7400):635-41.
• [18]Hedges SB, Dudley J, Kumar S: TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 2006, 22(23):2971-2.
• [19]Yang YF, Zhu T, Niu DK: Association of intron loss with high mutation rate in Arabidopsis: implications for genome size evolution. Genome Biol Evol 2013, 5(4):723-33.
• [20]Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, et al.: Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 2013, 45(8):884-90.
• [21]Roy SW, Fedorov A, Gilbert W: Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci U S A 2003, 100(12):7158-62.
• [22]Coulombe-Huntington J, Majewski J: Characterization of intron loss events in mammals. Genome Res 2007, 17(1):23-32.
• [23]Fawcett JA, Rouzé P, van de Peer Y: Higher intron loss rate in Arabidopsisthaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol Biol Evol 2012, 29(2):849-59.
• [24]Gao X, Lynch M: Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc Natl Acad Sci U S A 2009, 49:20818-23.
• [25]Kornblihtt AR, Schor IE, Allo M, Blencowe BJ: When chromatin meets splicing. Nat Struct Mol Biol 2009, 16(9):902-3.