Rooibos (Aspalathus linearis) genome size estimation using flow cytometry and k-mer analyses

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dc.contributor.authorMgwatyu, Yamkela
dc.contributor.authorStander, Allison Anne
dc.contributor.authorFerreira, Stephan
dc.date.accessioned2021-01-22T07:41:45Z
dc.date.available2021-01-22T07:41:45Z
dc.date.issued2020
dc.description.abstractPlant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos (Aspalathus linearis species complex) was estimated using DAPI flow cytometry and k-mer analyses. For flow cytometry, a suitable nuclei isolation buffer, plant tissue and a transport medium for rooibos ecotype samples collected from distant locations were identified. When using radicles from commercial rooibos seedlings, Woody Plant Buffer and Vicia faba as an internal standard, the flow cytometry-estimated genome size of rooibos was 1.24 ± 0.01 Gbp. The estimates for eight wild rooibos growth types did not deviate significantly from this value. K-mer analysis was performed using Illumina paired-end sequencing data from one commercial rooibos genotype. For biocomputational estimation of the genome size, four k-mer analysis methods were investigated: A standard formula and three popular programs (BBNorm, GenomeScope, and FindGSE). GenomeScope estimates were strongly affected by parameter settings, specifically CovMax.en_US
dc.identifier.citationMgwatyu, Y. et al. (2020). Rooibos (Aspalathus linearis) genome size estimation using flow cytometry and k-mer analyses. Plants, 9(2),270en_US
dc.identifier.issn2223-7747
dc.identifier.uri10.3390/plants9020270
dc.identifier.urihttp://hdl.handle.net/10566/5723
dc.language.isoenen_US
dc.publisherMDPIen_US
dc.subjectAspalathus linearisen_US
dc.subjectFlow cytometryen_US
dc.subjectGenome sizeen_US
dc.subjectITS regionen_US
dc.subjectRooibosen_US
dc.titleRooibos (Aspalathus linearis) genome size estimation using flow cytometry and k-mer analysesen_US
dc.typeArticleen_US

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