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. 2017 Jun 29;18(1):494.
doi: 10.1186/s12864-017-3856-6.

Diversity and evolution of mariner-like elements in aphid genomes

Maryem Bouallègue  1   2 , Jonathan Filée  1 , Imen Kharrat  2 , Maha Mezghani-Khemakhem  2 , Jacques-Deric Rouault  1 , Mohamed Makni  2 , Pierre Capy  3
Affiliations

Diversity and evolution of mariner-like elements in aphid genomes

Maryem Bouallègue et al. BMC Genomics. .

Abstract

Background: Although transposons have been identified in almost all organisms, genome-wide information on mariner elements in Aphididae remains unknown. Genomes of Acyrthosiphon pisum, Diuraphis noxia and Myzus persicae belonging to the Macrosiphini tribe, actually available in databases, have been investigated.

Results: A total of 22 lineages were identified. Classification and phylogenetic analysis indicated that they were subdivided into three monophyletic groups, each of them containing at least one putative complete sequence, and several non-autonomous sublineages corresponding to Miniature Inverted-Repeat Transposable Elements (MITE), probably generated by internal deletions. A high proportion of truncated and dead copies was also detected. The three clusters can be defined from their catalytic site: (i) mariner DD34D, including three subgroups of the irritans subfamily (Macrosiphinimar, Batmar-like elements and Dnomar-like elements); (ii) rosa DD41D, found in A. pisum and D. noxia; (iii) a new clade which differs from rosa through long TIRs and thus designated LTIR-like elements. Based on its catalytic domain, this new clade is subdivided into DD40D and DD41D subgroups. Compared to other Tc1/mariner superfamily sequences, rosa DD41D and LTIR DD40-41D seem more related to maT DD37D family.

Conclusion: Overall, our results reveal three clades belonging to the irritans subfamily, rosa and new LTIR-like elements. Data on structure and specific distribution of these transposable elements in the Macrosiphini tribe contribute to the understanding of their evolutionary history and to that of their hosts.

Keywords: Aphids; Comparative genomics; MITEs; Molecular evolution; Tc1-mariner; Transposable elements.

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Figures

Fig. 1
Fig. 1
Classification and phylogenetic tree of sequences identified in Macrosiphini tribe. a Classification of the 115 sequences obtained from Acyrthosiphon pisum, 45 from Diuraphis noxia and 23 from Myzus persicae. These 183 sequences, along with 146 elements belonging to the Tc1/mariner superfamily were classified using the UPGM-VM method [19]. References and positions of all these sequences are given in Additional file 3 according to the reading sense indicated by the arrow in the circular tree. Sequences found in A. pisum, D. noxia and M. persicae are given in colour, in green, brown and grey, respectively. Complete sequences are marked by a full black circle and MITEs by an empty circle. b The phylogeny based on amino-acid sequences of the 15 lineages. After a search of the best evolutionary scenario (ProTest 2.4), this tree was generated in MEGA6 with the Maximum likelihood (ML) method, using the WAG + F + I + G model. Only bootstrapping values (1000 replications) higher than 60% are written on the branch. Families and subfamilies are indicated in the right-hand part of the tree. The colored rectangles correspond to the different tribes as in A. Green squares, grey lozenges and brown triangles refer to the aphid species A. pisum, D. noxia and M. persicae, respectively. The designation of unpublished sequences extracted from other species than those of the three aphids includes a point (i.e. Vemar. from Vollenhovia emeryi). Sequences name: Apismar: elements from Acyrthosiphon pisum, Dnomar: elements from Diuraphis noxia and Mpmar: elements from Myzus persicae
Fig. 2
Fig. 2
Schematic representation of the 15 lineages corresponding to complete sequences found in aphid’s genomes. The elements are arranged and colored (as in Figure 1) according to the clades they belong to. Potentially active copies are marked with asterisks. The lack of TA (TSD) is marked by a slashed zero in red. Blue arrows indicate TIR, while bold lines represent UTRs. A turned T shows the presence of polyAdenylation site “AATAAA”. In transposase gene, the three catalytic residues containing aspartic amino acids marked in red are indicated. The helix turn helix (HTH) region, the nuclear localization signal (NLS), and motifs related to WVPHEL are also mentioned. Sequences name: Apismar: elements from Acyrthosiphon pisum, Dnomar: elements from Diuraphis noxia and Mpmar: elements from Myzus persicae
Fig. 3
Fig. 3
Multiple alignments of catalytic motifs of Tc1, mariner, maT families with the 15 lineages identified in aphids
Fig. 4
Fig. 4
Sequence alignments of MITE lineages with a longer autonomous partner. For each alignment (a-h), sequences are in blue, showing substitutions in red and gaps in black. The autonomous copies related to MITE and the global structure of the copies are shown on top, with arrowheads corresponding to TIR. Similar copies in length and sequence-defined sublineages (numbered in green). Given the lack of homology with the full potential element, MITE1.1 sub2 is not represented. a, c, e and h are found in A. pisum, b and d in M. persicae, f and g in D. noxia
Fig. 5
Fig. 5
Evolution analysis of different MITEs sublineages. Based on the comparison of consensus with copies, the similarity rates are identified. While copy sublineages with a high level of similarity present recent invasion, the decrease of this percentage refers to an ancient element. Filled, hatched and dotted patterns correspond to A. pisum, D. noxia and M. persicae, respectively. Colors match to the different tribes as in Fig. 1
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