LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions
Copia/Ale is the youngest lineage in both Solanum tuberosum and S. commersonii. Within it, we identified nightshade, a new LTR element active in the cultivated potato.
From an evolutionary perspective, long-terminal repeat retrotransposons (LTR-RT) activity during stress may be viewed as a mean by which organisms can keep up rates of genetic adaptation to changing conditions. Potato is one of the most important crop consumed worldwide, but studies on LTR-RT characterization are still lacking. Here, we assessed the abundance, insertion time and activity of LTR-RTs in both cultivated Solanum tuberosum and its cold-tolerant wild relative S. commersonii genomes. Gypsy elements were more abundant than Copia ones, suggesting that the former was somehow more successful in colonizing potato genomes. However, Copia elements, and in particular, the Ale lineage, are younger than Gypsy ones, since their insertion time was in average ~ 2 Mya. Due to the ability of LTR-RTs to be circularized by the host DNA repair mechanisms, we identified via mobilome-seq a Copia/Ale element (called nightshade, informal name used for potato family) active in S. tuberosum genome. Our analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in potato.
KeywordsExtrachromosomal circular DNA Insertion time Mobilome Potato Wild species
Long-terminal repeat retrotransposons
Depth of coverage
Extrachromosomal circular DNA
This work was carried out within the project “Development of potato genetic resources for sustainable agriculture” (PORES) funded by the University of Naples Federico II (Project ID: E76J17000010001). We are grateful to Mr. Raffaele Garramone for his technical assistance. No conflict of interest declared.
- De Haan S, Rodriguez F (2016) Potato origin and production. In: Singh J, Kaur L (eds) Advances in potato chemistry and technology. Elsevier, London, pp 1–32Google Scholar
- Esposito S, D’Amelia V, Carputo D, Aversano R (2019b) Genes involved in stress signals: the CBLs-CIPKs network in cold tolerant Solanum commersonii. Biol Plant. https://doi.org/10.32615/bp.2019.072
- Jiang N, Visa S, Wu S, Van Der Knaap E (2012) Rider transposon insertion and phenotypic change in tomato. In: Grandbastien MA, Casacuberta JM (eds) Plant Transposable Elements, Topics in Current Genetics, Heidelberg. Springer-Verlag, Berlin, pp 297–312Google Scholar
- Leisner CP, Hamilton JP, Crisovan E, Manrique-Carpintero NC, Marand AP, Newton L, Pham GM, Jiang J, Douches DS, Jansky SH, Buell CR (2018) Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. Plant J 94:562–570CrossRefGoogle Scholar
- Piegu B, Guyot R, Picault N, Roulin A, Sanyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, Panaud O (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262–1269CrossRefGoogle Scholar