LI-Seq: A Cost-Effective, Low Input DNA method for Whole Genome Library Preparation

Abstract

Samples from species of high conservation concern are often low in total genomic DNA. Whole Genome Sequencing (WGS) can provide many insights that can be used to aid in species conservation, but current methods for working with low quality and low input samples can be cost prohibitive for population level genomic analyses. Thus, there is an urgent need for a cost-effective method of preparing WGS libraries from low input DNA samples. To bridge the gap between sampling techniques commonly used in conservation genetics that yield low quality and low input DNA and the powerful tool of WGS, we developed LI-Seq, a more efficient method that successfully produces libraries from low quality DNA with as low input as 0.48 ng of DNA, with an average final library size of 300-500 base pairs. Sequencing results suggest no difference in sequencing quality or coverage between low quality, low input and high quality, high input starting material using our protocol. We conclude that our new method will facilitate high-throughput WGS on low quality, low input samples, thus expanding the power of genomic tools beyond traditional high quality samples.

Limited domestic introgression in a final refuge of the wild pigeon

“…Library preparation used the MGISP-100 automated system, and sequencing was conducted using the BGISEQ-500 platform ( Huang et al., 2017 ), using paired end 150-bp sequence reads. Library preparation of all other samples was carried out by TMS using a protocol designed for increased efficiency when using low-input DNA ( Schweizer et al., 2021 ). DNA samples were quantified using a Qubit 2.0 (Invitrogen, Waltham, Massachusetts, USA).…”

Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum

“…Libraries were prepared using a modified Illumina Nextera library preparation protocol [62] and then sequenced on either an Illumina HiSeq platform or Illumina NovaSeq 6000 using paired-end sequencing of 150 bp reads. De novo assembly of full mitochondrial protein-coding gene sets (13 genes) was conducted using NOVOplasty v4.3.1 [63].…”

Population genetic consequences of the seasonal migrations of birds

“…Libraries were prepared using a modified Illumina Nextera library preparation protocol (66,67) and then sequenced on either an Illumina HiSeq or Illumina NovaSeq 6000 platform using paired-end sequencing of 150 bp reads. Libraries were prepared using a modified Illumina Nextera library preparation protocol (66,67) and then sequenced on an Illumina HiSeq, NovaSeq 6000, or NovaSeq X platform using paired-end sequencing of 150 bp reads. Libraries used in analyses produced an average of 32 million ± 10 million reads per sample (range 7 million-156 million).…”