Biology subjects

Jones, E. R.

Publications and source records attributed to Jones, E. R..

3 recordsLinked to original sources

bioRxiv2020

A curated dataset of modern and ancient high-coverage shotgun human genomes.

Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of capture SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain type of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 34 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 73,435,604 sites called across 18 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.

genomics↗

bioRxiv2019

Removing reference bias in ancient DNA data analysis by mapping to a sequence variation graph

BackgroundDuring the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Recently, alternative approaches for read mapping and genetic variation analysis have been developed that replace the linear reference by a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for ancient DNA and compare our approach to existing methods. ResultsWe used vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants, and compared these with the same data aligned with bwa to the human linear reference genome. We show that use of vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias, but can have lower sensitivity than vg, particularly for indels. ConclusionsOur findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analysing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.

genomics↗

bioRxiv2017

Altering Expression Of A Vacuolar Iron Transporter Doubles Iron Content In White Wheat Flour

Iron deficiency anaemia is a major global health issue, which has prompted mandatory fortification of cereal products with iron salts or elemental iron in many countries around the world. Rather than post-harvest fortification, biofortification - increasing the intrinsic nutritional quality of crops - is a more sustainable way of alleviating nutrient deficiencies. To identify target genes for biofortification of wheat (Triticum aestivum), we functionally characterized homologues of the Vacuolar Iron Transporter (VIT). The wheat genome contains two VIT paralogues, TaVIT1 and TaVIT2, which have different expression patterns, but are both low in the endosperm. TaVIT2, but not TaVIT1, was able to transport iron in a yeast complementation assay. TaVIT2 also transported manganese but not zinc. By over-expressing TaVIT2 under the control of an endosperm-specific promoter, we achieved a 2-fold increase in iron in white flour fractions, exceeding minimum UK legal fortification levels. The highiron trait was consistent across independent lines and was stable in the next generation and in two different growth conditions. The single-gene approach impacted minimally on plant growth and was also effective in barley. The anti-nutrient phytate was not increased in white flour from the cisgenic wheat lines, suggesting that food products made from it could contribute to improved iron nutrition.

plant biology↗