Sequencing and assembling the allotetraploid genome of the apomictic grass E. curvula

CARBALLO J; GARBUS I; ZAPPACOSTA D; GALLO C A; SELVA JP; CACCAMO M; ECHENIQUE V

Evento virtual

Simposio; 5to Simposio Argentino de Jóvenes Investigadores en Bioinformática; 2020

The Argentine Regional Student Group

Eragrostis curvula (weeping lovegrass) is species native from Southern Africa with different ploidy levels ranging from 2X to 8X and with a haploid chromosome number of ten. Despite its importance as forage crop weeping lovegrass has been studied as model of diplospory apomixis. Apomixis is a way of reproduction where the progeny result genetically identical to the mother plant. This trait has been highlighted as the holy grail of the agriculture since the transference to economically important crops as rice, wheat or corn would transform the agriculture as we know today. The aim of this work was to sequence and assembly the allotetraploid cultivar (2n=4x=40, 1,200 Mb) of E. curvula Don Walter to generate the genomic resource necessary to develop the apomixis synthetic technology.The genome was sequenced through Chromium 10x technology and one cell of Oxford nanopore. The 10X platform render 424,3 millions of 2x150 raw illumina reads representing 106.09X of coverage of the haploid genome while the nanopore sequences result in 1,864,546 long reads with an N50 of 17,217 and a coverage of 8.93X. The supernova software was used to assembled the 10x reads alone obtaining a genome assembly with a N50 of 8,480 bp a genome size of 833.5 Kb and 65% of the complete busco genes. The integration of this assembly with the nanopore reads was made with DBG2OLC software and polished with the Pilon. The final assembly length was 1,147.8 Mb distributed in 7,542 contigs, the N50 was 224.3 Kb and the complete BUSCO genes increase to 96.9%. The gene annotation of this genome was made with maker software obtaining 124,538 transcripts representing 96.1% of the BUSCO genes (single 56.0%, duplicated 40.1%).The contiguity of this genome will be improved adding more nanopore data, however the results obtained here demonstrate that a hybrid and inexpensive approach can be used to obtain a high quality genome assembly. This is the first apomictic genome sequenced so far and will be used as resource to find candidate genes for apomixis.