Nothofagus pumilio (Lenga) genome sequencing as a resource for interdisciplinary and systemic studies in a context of Global Climate Change

CAROLINA SOLIANI; NICOLAS BELLORA; TOMAS MOYANO; RODRIGO GUTIERREZ; MAXIMILIANO ESTRAVIS-BARCALÁ; MARÍA VERÓNICA ARANA

Mendoza

Congreso; 10° Congreso Argentino de Bioinformática y Biología Computacional; 2019

Asociación Argentina de Bioinformática y Biología Computacional

Genomic approaches represent an important first step and tool for studying organisms biology under laboratory or natural conditions. From a productive point of view, the genomesequence can accelerate breeding and facilitate the study of complex, quantitative traits. It is also possible, for productive as well as ecological purposes, to develop novel genomic markers for population studies. Finally, genomic information allows for the identification and characterization of new genes and metabolic pathways. Moreover, it can help understand the genetic mechanisms that regulate the organism?s responses to changing environments.Nothofagus pumilio (lenga) is an endemic tree of the southern temperate forests of Argentina and Chile. It constitutes a key ecological species, distributed across a wide latitudinal and altitudinal range. Despite its economic and ecological importance, genomic resources for N. pumilio and the whole genus are scarce. In this work, we present the first results related to the complete genome sequencing of N. pumilio. This species is diploid 2n=26, and has no whole-genome information available in public databases. This will be the first sequenced genome for a native tree of Argentina and Chile.Using flow cytometry, the size of the haploid genome of N. pumilio was estimated inapproximately 790 Mb (1.61 pg/nucleus). We followed a mixed strategy with the aim of achieving a first draft genome of N. pumilio. We combined Oxford Nanopore Technologies (ONT) MinION reads and paired-end (PE) and mate-pair (MP) Illumina libraries, with different read lengths (350 and 550 bp for PE, and 5 kb for MP). We plan to complement these sequences with PacBio long reads and Optical Mapping. ONT sequencing yielded 784.606 reads with N50=4887, totaling 1.8 Gb. Each of the PE and MP libraries yielded around 40X coverage of the estimated haploid genome. More than 88% of Illumina reads have a Phred score greater than 30. We present and discuss preliminary analyses of read quality, nucleotide composition and distribution, and k-mer and heterozygosity analyses, together with a proposed downstream pipeline for assembly. Our Argentinian-Chilean collaborative effort will pave the way for a milestone genomicresource for an iconic South American tree species.