Hi

We recently have a similar problem for spider samples and with nanopore sequencing that is much more sensitive to A260/230 than other platforms. In our case we thought it might be due to the quitin of the spiders that is really saturated with carbohydrates. The A260/230 might also be low if there are phenol residues (phenol-cloroform extraction), guanidin (column extraction) or glycogen .

Anyways what we used was the Qiagen Genomic DNA for blood an tissue kit. We made 4 washes with elution buffer instead of 3 and 2 washes wit cold ethanol. Also, we did not perform the initial vortex and centrifugation post lysis.

Illumina recommends assess the quality of gDNA throught the calculation of the Genomic Quality Number (GQN) using Fragmen Analyzer. Values greater than 9 will indicate a good quality.

https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/library-qc-fragment-analyzer-application-note-770-2017-002.pdf

I recently extracted gDNA from a sea anemone for PacBio sequencing and had low 260/230 ratios (which I attributed to the pigmentation of these animals) following a proteinase K digestion followed by salt-chloroform extraction. My 260/280 ratios were good and samples were high MW. Given the low 260/230 ratio I performed a second clean-up using the Qiagen Genomic-Tip 20/G kit. Following this, my 260/230 ratios were then higher than recommended (>2.3). I submitted the samples anyway and have received good data back. I would therefore recommend the Qiagen genomic tip system for a clean-up of your samples if you have concerns about contaminants affecting this ratio.

Thanks Craig S Wilding and Silvia Hinojosa-Alvarez . It looks like I'm left with two options; re-extract sample or clean-up. I'll mull this over to pick the best option for me.

Thanks for the input Victor M. Guerrero-Sanchez , however my lab doesn't have a fragment analyzer. I was more looking for advice given the tools I have (Nanodrop & Qubit).