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Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii

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Abstract

Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C3 grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp. It is a promising feedstock for second-generation biofuels and biomethane production. To identify and characterize the most repetitive TEs in the genomes of A. donax and its ancestral A. plinii species, we carried out low-coverage whole genome shotgun sequencing for both species. Using a de novo repeat identification approach, 33,041 and 28,237 non-redundant repetitive sequences were identified and characterized in A. donax and A. plinii genomes, representing 37.55 and 31.68% of each genome, respectively. Comparative phylogenetic analyses, including the major TE classes identified in A. donax and A. plinii, together with rice and maize TE paralogs, were carried out to understand the evolutionary relationship of the most abundant TE classes. Highly conserved copies of RIRE1-like Ty1-Copia elements were discovered in two Arundo spp. in which they represented nearly 3% of each genomic sequence. We identified and characterized the medium/highly repetitive TEs in two unexplored polyploid genomes, thus generating useful information for the study of the genomic structure, composition, and functioning of these two non-model species. We provided a valuable resource that could be exploited in any effort aimed at sequencing and assembling these two genomes.

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Authors and Affiliations

  1. Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà, 33, 56127, Pisa, Italy

    Aung Kyaw Lwin, Edoardo Bertolini, Mario Enrico Pè & Andrea Zuccolo

  2. Sugarcane Research and Seed Farm, Pyinmana, Nay Pyi Taw, Myanmar

    Aung Kyaw Lwin

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  1. Aung Kyaw Lwin
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  2. Edoardo Bertolini
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  3. Mario Enrico Pè
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  4. Andrea Zuccolo
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Correspondence to Andrea Zuccolo.

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Data availability

The raw sequence data used to analyze Arundo spp. were submitted to GenBank under the BioSample Accession Numbers SAMN05853577 and SAMN05853578. Repeat libraries and sequence alignments supporting the conclusions of this research are listed in the “Additional Files” section.

Funding

This project was funded by the Scuola Superiore Sant’Anna, Pisa, Italy (APOMIS11AZ) and by the Doctoral School of Life Sciences of the Scuola Superiore Sant’Anna, Pisa, Italy. We thank Dr. Roberto Pilu from Milan University, Italy, for kindly providing A. donax and A. plinii fresh leaf tissue.

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The authors declare that they have no competing interests.

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This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Library Donax_pri_repeat_1610_library: A.donax primary TE library (FA 376 kb)

Library Plinii_pri_repeat_1963_library: A. plinii primary TE library (FA 747 kb)

Library Donax_ctgs_33041_lib: A. donax extended TE library (ZIP 4957 kb)

Library Plinii_ctgs_28237_lib: A. plinii extended TE library (ZIP 3906 kb)

438_2016_1263_MOESM5_ESM.png

Dot plot comparisons of three A. donax repetitive contigs with (a) RIRE1 (complete element) (b) Copia-16_SB (internal region) (c) RLG_sclvana_6_1 (internal region) elements at nucleotide level using Dotter. A copy of 5’ has been added to the 3’ LTR of contig 19571 (PNG 102 kb)

Donax_RIRE1.fsa: complete A. donax RIRE1 like sequence (fsa 8 kb)

438_2016_1263_MOESM7_ESM.meg

Copia_DPMR.meg: multiple alignment of Ty1-Copia RT paralogous sequences identified in Arundo spp., Rice and Maize (MEG 112 kb)

438_2016_1263_MOESM8_ESM.meg

Gypsy_DPMR.meg: multiple alignment of Ty3-Gypsy RT paralogous sequences identified in Arundo spp., Rice and Maize (MEG 161 kb)

438_2016_1263_MOESM9_ESM.pdf

Ty1-Copia-detailed.pdf: NJ tree of Ty1-Copia RT paralogous sequences identified in Arundo spp., Rice and Maize. It shows sequence names (PDF 238 kb)

438_2016_1263_MOESM10_ESM.pdf

Ty3-Gypsy-detailed.pdf: NJ tree of Ty3-Gypsy RT paralogous sequences identified in Arundo spp., Rice and Maize. It shows sequence names (PDF 439 kb)

CACTA.meg: multiple alignment of CACTA paralogous sequences identified in Arundo spp., Rice and Maize (MEG 18 kb)

MuDR.meg: multiple alignment of MuDR paralogous sequences identified in Arundo spp., Rice and Maize (MEG 5 kb)

438_2016_1263_MOESM13_ESM.fa

TE_tracts.fa: multifasta file including the tracts of TE coding domains used as queries in similarity searches to retrieve copies of TE paralogous (FA 1 kb)

438_2016_1263_MOESM14_ESM.pdf

COPIA_ctg.pdf: NJ tree of Ty1-Copia RT paralogous sequences identified in extended repetitive libraries for both Arundo species (PDF 81 kb)

438_2016_1263_MOESM15_ESM.pdf

GYPSY_ctg.pdf: NJ tree of Ty3-gypsy RT paralogous sequences identified in extended repetitive libraries for both Arundo species (PDF 138 kb)

438_2016_1263_MOESM16_ESM.pdf

CACTA_ctg.pdf: NJ tree of CACTA transposase paralogous sequences identified in extended repetitive libraries for both Arundo species (PDF 20 kb)

438_2016_1263_MOESM17_ESM.pdf

MUDR_ctg.pdf: NJ tree of MuDR transposase paralogous sequences identified in extended repetitive libraries for both Arundo species (PDF 9 kb)

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Lwin, A.K., Bertolini, E., Pè, M.E. et al. Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii . Mol Genet Genomics 292, 157–171 (2017). https://doi.org/10.1007/s00438-016-1263-3

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