COMPLETE CHLOROPLASTIC AND MITOCHONDRIAL GENOMES OF A NATIVE TREE SPECIES AND STRATEGIES TOWARD END-TO-END CHROMOSOMAL ASSEMBLY

MAXIMILIANO ESTRAVIS-BARCALA; TOMÁS MOYANO; MARÍA VERÓNICA ARANA; RODRIGO A. GUTIÉRREZ; NICOLAS BELLORA

Congreso; SAIB-SAMIGE 2020; 2020

Sociedad Argentina de Investigación en Bioquímica y Biología Molecular

Nothofaguspumilio(common name: lenga) is the most abundant tree of the southerntemperate forests of Argentina and Chile. It constitutes a keyecological species, distributed across a wide latitudinal andaltitudinal range. Despite its economic and ecological importance,genomic resources for N.pumilioand the whole genus are scarce. This bi-national iniciative aims atsequencing and assembling the complete genome of N.pumilio,which will be the first such resource for a native tree of Argentinaand Chile.Asa first step toward this goal, total DNA was extracted from budscollected from an individual in the Argentina-Chile border in MonteTronador. Paired-end (PE) and mate-pair (MP) Illumina libraries withdifferent read lengths (350 and 550 bp for PE, and 5 kb for MP) wereconstructed and sequenced. Each of the PE and MP libraries yieldedaround 40X coverage of the estimated haploid genome (790 Mb usingflow citometry), and more than 88% of Illumina reads had a Phredscore greater than 30. In order to assemble the organellar genomes,reads were mapped to reference plant cpDNA or mtDNA, and severalreads were chosen as seeds. This strategy takes advantage of the highsequence conservation of cpDNA and mtDNA among plant species. Then,each genome was assembled separately by an overlap-extension method.In this work we present N.pumiliocpDNA (150,390 bp) and mtDNA (354,003 bp). Both genomes wereannotated against reference species and feature all rRNA and tRNAgenes, apart from all expected protein-coding genes found in mostplant species. Moreover, the cpDNA has a typical structure of twoinverted repeats (IRA and IRB) which separate a Long Single Copysection (LSC) and a Short Single Copy section (SSC).Atthe same time, a preliminary denovototal assembly was performed using Redundans (with all PE reads asinput) and Opera (for scaffolding with MP reads). This assemblyyielded 13,140 scaffolds longer than 2000 bp, adding to 360,574,575bp. About 90% of PE and MP reads were used in the assembly. A totalof 2326 eukaryotic BUSCOs were searched in the genome assembly, ofwhich 2040 (87.7%) were complete, and only 168 (7.2%) missing.Moreover, 90% of reads from a previous N.pumiliotranscriptomic study were uniquely mapped to the new assembly.However, the assembly is about half the expected size according toflow citometry. These results suggest that we were able to capturevirtually all coding, high-complexity regions of the genome, but manyrepetitive or otherwise low-complexity regions are being collapsed orincorrectly assembled. In this work we discuss some possible futuresteps aiming at completing the genome assembly, mainly HiC forend-to-end chromosome structure and PacBio HiFi sequencing forrepetitive regions resolution. These newly assembled genomesconstitute the first genomic resources for N.pumilioand will be useful for population and biochemical studies in thisspecies and its relatives.p { margin-bottom: 0.1in; direction: ltr; color: #00000a; line-height: 120%; text-align: left; orphans: 2; widows: 2 }p.western { font-family: "Liberation Serif", serif; font-size: 12pt; so-language: en-US }p.cjk { font-family: "DejaVu Sans"; font-size: 12pt; so-language: zh-CN }p.ctl { font-family: "FreeSans"; font-size: 12pt; so-language: hi-IN }a.cjk:link { so-language: zxx }a.ctl:link { so-language: zxx }