Fig 1.
Schematic representation of representative LTR retrotransposons.
The main characteristics of autonomous and non-autonomous elements are represented. LTR-retrotransposons have long terminal repeats (LTRs) in direct orientation. Autonomous elements contain at least two genes, called gag and pol. The gag gene encodes a capsid-like protein and the pol gene encodes a polyprotein that is responsible for protease (PR), reverse transcriptase (RT), RNase H (RH) and integrase (INT) activities. PBS, primer binding site; PPT, polypurine track. Non-autonomous elements, such as large retrotransposon derivatives (LARDs) and terminal repeat retrotransposons in miniature (TRIMs), lack most or all coding sequence. Non-LTR retrotransposons are divided into long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). LINE coding regions include a gag-like protein (ORF), an endonuclease (EN) and reverse transcriptase (RT). Both LINEs and SINEs usually terminate by a poly(A) sequence [5]. Thick lines below the elements indicate the sequences amplified in lentil in this work; the first letter c in the nomenclature indicates that the sequence was identified as a copia and g as a gypsy element. Drawings not made to scale.
Fig 2.
Genetic map obtained with markers showing Mendelian segregations.
The markers from the parental L. culinaris Lupa are indicated in red, that is, these bands were observed in the parental Lupa but were absent in the other parental, and vice versa for markers in black. Linkage groups are numbered from LG1 to LG8. A LOD score of 4 was used. Markers preceded by a P are iPBSs, by R are REMAPs and S indicates the SSR markers included. Partial distances in cM are indicated to the left of LGs while the total LG distance is displayed at the bottom. The insert to the right corresponds to the boxplot distribution of the distance in cM between consecutive markers.
Table 1.
Partial retrotransposon sequences obtained from lentil cultivar Lupa.
Fig 3.
Phylogenetic trees of reverse transcriptase sequences.
Trees show the relationships between lentil sequences and Medicago truncatula (Mtr) sequences. A, Ty1-copia sequences; B, Ty3-gypsy sequences. Lentil sequences are within boxes indicating the different linkage groups (Gr) to which they belong, groups were related to the M. truncatula clades as described by Piednöel et al. [46] and the M. truncatula sequence numbers as in Wang and Liu [44]. Red color denotes the presence of premature stop codons in the reading frames.
Table 2.
Retrotransposon long terminal repeat sequences amplified from lentil cultivar Lupa.
Table 3.
Number of in silico hits of lentil retrotransposon sequence types in relation to distances between consecutive hits.
Fig 4.
Contig length (bp) density distribution.
Figure shows the distributions of contig lengths; blue and red color lines indicate contigs with at least one lentil LTR-RT sequence or 10 or more lentil LTR-RT, respectively. The black line indicates the distribution of all lentil contigs, V0.8 genome. n = number of contigs.
Fig 5.
Boxplot distributions of contig length according to the number of “hits” generated by the lentil LTR-RT sequences.
Numbers at the bottom indicate the number of hits per contig while those on top to the number of contigs in each class. The first distribution was obtained when two hits were considered different if they were separated by at least 10 bp, the second distribution when hits were separated by at least 10,000 bp.
Fig 6.
Goodness of fit testing a Poisson distribution of the LTR-RT number according to the square root of the number of contigs.
The continuous line indicates the theoretical distribution and bars the real number of contigs within of each class. A between hit distance of > 10,000 bp was considered.
Fig 7.
Diagram of the contigs in the lentil genome containing the highest number of LTR-RT sequences.
Contig size (above) and contig name (below) are indicated. Arrows indicate sequences’ orientations. Blue boxes indicate putative RT flanked by two LTRs, red boxes indicate the presence of a reverse transcriptase sequence between LTRs. LTR are named according to their lineage (Table 2) and the internal sequences according to the nomenclature used in Table 1.