Leveraging whole genome sequencing to estimate telomere length in plants

Abstract

Changes in telomere length are increasingly used to indicate species’ response to environmental stress across diverse taxa. Despite this broad use, few studies have explored telomere length in plants. However, rapid advances in sequencing approaches and bioinformatic tools now allow estimation of telomere length using whole genome sequencing (WGS) data. Thus, evaluation of new approaches for measuring telomere length in plants are needed. Traditionally, telomere length has been quantified using quantitative polymerase chain reaction (qPCR). While WGS has been extensively used in humans, no study to date has compared the effectiveness of WGS in estimating telomere length in plants relative to traditional qPCR approaches. In this study, we use one hundred Populus clones re-sequenced using short-read Illumina sequencing to quantify telomere length using three different bioinformatic approaches, Computel, K-seek, and TRIP, in addition to qPCR. Overall, telomere length estimates varied across different bioinformatic approaches, but were highly correlated across methods for individual genotypes. A positive correlation was observed between WGS estimates and qPCR, however, Computel estimates exhibited the greatest correlation. Computel incorporates genome coverage into telomere length calculations, suggesting that genome coverage is likely important to telomere length quantification when using WGS data. Overall, telomere estimates from WGS provided greater precision and accuracy of telomere length estimates relative to qPCR. The findings suggest WGS is a promising approach for assessing telomere length, and as the field of telomere ecology evolves may provide added value to assaying response to biotic and abiotic environments for plants needed to accelerate plant breeding and conservation management.

Telomere Length in Plants Estimated with Long Read Sequencing

“…Methods to more extensively, accurately, and reproducibly measure telomere length have not been developed until more recently. Illumina short read whole genome sequencing is emerging as an alternative approach to establish telomere length (Paez, Holliday and Hamilton, 2023), and as long read sequencing technology continues to improve, telomere to telomere (T2T) genome assemblies have also become possible (see discussion). The advent of Oxford Nanopore Technology (ONT) long read single molecule sequencing has enabled the ability to resolve the length of telomere repeats directly in our genome assemblies.…”