Open Access Research article

Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes

Jean-Luc Da Lage1*, Manfred Binder2, Aurélie Hua-Van1, Štefan Janeček3 and Didier Casane14

Author Affiliations

1 Laboratoire Evolution, génomes et spéciation UPR 9034 CNRS, 91198 Gif-sur-Yvette, and Université Paris-Sud, Orsay, 91405, France

2 CBS Fungal Biodiversity Centre, Evolutionary Phytopathology, Institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Uppsalalaan 8, Utrecht, CT, 3584, The Netherlands

3 Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Science, Dubravska cesta 21, Bratislava, SK-84551, Slovakia

4 Université Paris Diderot, Sorbonne Paris Cité, France

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BMC Evolutionary Biology 2013, 13:40  doi:10.1186/1471-2148-13-40

Published: 13 February 2013

Additional files

Additional file 1: Table S1:

List of primers designed for detection of α-amylase genes orthologous to Phchr1|7087|. PCR conditions were: initial denaturation 94°C, 6 mn; denaturation 94°C, 25 s; annealing 58°C, 50s; elongation 72°C, 1 mn, 45 cycles using the Taq Gold polymerase (Applied Biosystems). Various combinations of forward and reverse primers were tried.

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Additional file 2: Table S2:

GenBank or JGI accession numbers of sequences EF1α, RNA polymerase II LSU 1 and LSU2, used for datation estimates.

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Additional file 3: Table S3:

Abbreviations used in Figure 1, and JGI or Uniprot accession numbers. Colors are as in Figure 1.

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Additional file 4: Figure S1:

Alignment of the α-amylase protein sequences studied, built with MAFFT, showing the intron positions. Pink: phase 0 introns; green: phase 1 introns; blue: phase 2 introns. This alignment was used, without the N-terminal variable region (signal peptide), for gene tree reconstruction (Additional file 5: Figure S2). Intron-slided introns are not shown.

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Additional file 5: Figure S2:

Gene tree drawn from maximum likelihood reconstruction and 100 bootstrap replicates (see text). The tree was rooted with two bacterial sequences. Abbreviations are given in Additional file 2: Table S1.

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Additional file 6: Figure S3:

Reconciliation tree made from the gene tree (Additional file 5: Figure S2) and the species tree (Additional file 7: Figure S4) with Notung 2.6. The letter D indicate gene duplications, grey branches are lost genes. Orange lines are weak edges.

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Additional file 7: Figure S4:

Fungal species tree and divergence times estimated with BEAST using EF1α+LSU1+LSU2, with dates of divergence at nodes. Horizontal bars show the 95% highest posterior intervals of the divergence times.

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Additional file 8: Table S4:

Analysis of exon size distribution. For each gene, the effective number of exon was computed according to ref. 16. The statistical significance was estimated by 10,000 simulations. Ne: effective number of exons. ns: not significant; *: p<0.05. 5%: value of Ne below which are the smallest 5% simulated Ne values; 95%: value of Ne below which are the smallest 5% simulated Ne values.

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Additional file 9: Figure S5:

Consensus sequences at positions -2 and -1, and +1 and +2 around intron positions with different phases, drawn with Weblogo 3.2 [72]. n is the number of sequences. Error bars are as in Figure 6. A: Phase 0 positions, in the presence of intron; B: Phase 1 positions, in the presence of intron; C: Phase 2 positions, in the presence of intron; D: phase 0 positions, in the absence of intron; E: phase 1 positions, in the absence of intron; F: phase 2 positions, in the absence of intron.

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Additional file 10: Figure S6:

Consensus splicing sites of introns drawn with Weblogo 3.2 [72]. Left to the vertical dashed line: first five nucleotides of the 5' splicing site; right to the vertical dashed line: last three nucleotides of the 3' splicing. n is the number of sequences. Error bars are as in Figure 6. A: global consensus; B: conserved old introns; C: recent introns; D: position 30; E: position 56; F: introns of Heterobasidion annosum; G: introns of Punctularia strigosozonata.

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