Read data improvement approaches for genome assembly of non‑model plant species

Emirsaliev A.; Afonnikov D.; Mitrofanova I.; Salina E.

Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia; N.V. Tsitsin Main Botanical Garden of Russian Academy of Science, 127276 Moscow, Russia

emirsaleh@bionet.nsc.ru

Assembling genome of non-model plant species is often challenging because of large size of nuclear genome, high repetitive content, varying ploidy levels, high heterozygosity and absence of high-quality genomic or transcriptomic data for close relatives. The approaches discussed are particularly valuable for non-model species where sample availability, funding, or technical constraints limit sequencing options. The computational cost of read reprocessing is minimal compared to additional sequencing rounds, making these strategies accessible to small research groups. Approaches discussed in the study facilitates obtaining a draft genome assembly and could assist in decision on what kind of data to be resequenced is yet still needed for “clean” result.