An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes
Castanera, Raúl (Centre de Recerca en Agrigenòmica)
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica)
Pujol Abajo, Marta (Centre de Recerca en Agrigenòmica)
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)

Date:	2020
Abstract:	The published melon (Cucumis melo L. ) reference genome assembly (v3. 6. 1) has still 41. 6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches have been undertaken to improve the melon genome assembly in recent years, the high percentage of repeats (~40%) and limitations due to read length have made it difficult to resolve gaps and scaffold's misassignments to pseudomolecules, especially in the heterochromatic regions. Taking advantage of the PacBio single- molecule real-time (SMRT) sequencing technology, an improvement of the melon genome was achieved. About 90% of the gaps were filled and the unassigned sequences were drastically reduced. A lift-over of the latest annotation v4. 0 allowed to re-collocate protein-coding genes belonging to the unassigned sequences to the pseudomolecules. A direct proof of the improvement reached in the new melon assembly was highlighted looking at the improved annotation of the transposable element fraction. By screening the new assembly, we discovered many young (inserted less than 2Mya), polymorphic LTR-retrotransposons that were not captured in the previous reference genome. These elements sit mostly in the pericentromeric regions, but some of them are inserted in the upstream region of genes suggesting that they can have regulatory potential. This improved reference genome will provide an invaluable tool for identifying new gene or transposon variants associated with important phenotypes.
Grants:	Ministerio de Economía y Competitividad AGL2015-64625-C2-1-R Ministerio de Economía y Competitividad SEV-2015-0533 Ministerio de Economía y Competitividad AGL2016-78992-R
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Frontiers in plant science, Vol. 10 (January 2020) , art. 1815, ISSN 1664-462X

DOI: 10.3389/fpls.2019.01815
PMID: 32076428

10 p, 1.1 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles