Abstract
Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic analyses.
Highlights
Lentil (Lens culinaris Medik. subsp. culinaris) is one of the earliest domesticated plant species in the Fertile Crescent
The inter-primer binding site (iPBS) markers were used in the genetic linkage analysis and to sequence and identify some retrotransposon long terminal repeats (LTRs)
In total 741 bands were scored of which 233 iPBS evidenced polymorphism between L. c. culinaris and L. c. orientalis
Summary
Lentil (Lens culinaris Medik. subsp. culinaris) is one of the earliest domesticated plant species in the Fertile Crescent. Culinaris) is one of the earliest domesticated plant species in the Fertile Crescent It is a diploid (2n = 14), self-pollinated annual cool season grain legume normally grown in temperate semi-arid regions, usually in rotation with cereals. The crop is widely cultivated throughout Western Asia, Northern Africa, the Indian subcontinent, Australia and North America [1,2]. This species is included in the tribe Fabeae or Vicieae, which includes the genera Lathyrus, Pisum, Vavilovia and Vicia [3,4]. Retrotransposons (RTs) are the most abundant and widespread class of eukaryotic TEs and are widely distributed along plant genomes [6,7]. In the legume model species Medicago truncatula RT coverage corresponded to 26% and in the chickpea crop (Cicer arietinum) amounted to 49% [8], while in the Vicieae species comprised up to 81% of the nuclear genome [9]
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