Biology subjects

Lavington, E.

Publications and source records attributed to Lavington, E..

4 recordsLinked to original sources

bioRxiv2023

Herpes-like viral elements and universal subtelomeric ribosomal RNA genes in a chromosome-scale thraustochytrid genome assembly

We used long-read sequencing to produce a telomere-to-telomere genome assembly for the heterotrophic stramenopile protist Aurantiochytrium limacinum MYA-1381. Its [~]62 Mbp nuclear genome comprises 26 linear chromosomes with a novel configuration: subtelomeric rDNAs are interspersed with long repeated sequence elements denoted as LOng REpeated - TElomere And Rdna Spacers (LORE-TEARS). These repeats may play a role in chromosome end maintenance. A [~]300 Kbp circular herpesvirus-like genomic element is present at a high copy number. A 269 Kbp related virus-like element was found to reside between two complete sets of rRNA and LORE-TEAR sequences on one end of chromosome 15, indicating recent recombination between the viral and nuclear genome. Our data reveal new types of giant endogenous viral elements originating from herpes-like viruses and existing as either stand-alone or integrated elements.

genomics↗

bioRxiv2021

Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination, and reassortment, factors such as climate, agriculture practices, and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C[->]T and G[->]A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5 intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over 6 vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.

plant biology↗

bioRxiv2019

A comprehensive genealogy of the replication associated protein of CRESS DNA viruses reveals a single origin of intron-containing Rep

Abundant novel circular Rep-encoding ssDNA viruses (CRESS DNA viruses) have been discovered in the past decade, prompting a new appreciation for the ubiquity and genomic diversity of this group of viruses. Although highly divergent in the hosts they infect or are associated with, CRESS DNA viruses are united by the homologous replication-associated protein (Rep). An accurate genealogy of Rep can therefore provide insights into how these diverse families are related to each other. We used a dataset of eukaryote-associated CRESS DNA RefSeq genomes (n=926), which included representatives from all six established families and unclassified species. To assure an optimal Rep genealogy, we derived and tested a bespoke amino acid substitution model (named CRESS), which outperformed existing protein matrices in describing the evolution of Rep. The CRESS model-estimated Rep genealogy resolved the monophyly of Bacilladnaviridae and the reciprocal monophyly of Nanoviridae and the alpha-satellites when trees estimated with general matrices like LG did not. The most intriguing, previously unobserved result is a likely single origin of intron-containing Reps, which causes several geminivirus genera to group with Genomoviridae (bootstrap support 55%, aLRT SH-like support 0.997, 0.91-0.997 in trees estimated with established matrices). This grouping, which eliminates the monophyly of Geminiviridae, is supported by both domains of Rep, and appears to be related to our use of all RefSeq Reps instead of subsampling to get a smaller dataset. In addition to producing a trustworthy Rep genealogy, the derived CRESS matrix is proving useful for other analyses; it best fit alignments of capsid protein sequences from several CRESS DNA families and parvovirus NS1/Rep sequences.

evolutionary biology↗

bioRxiv2017

The effect of common inversion polymorphisms In(2L)t and In(3R)Mo on patterns of transcriptional variation in Drosophila melanogaster

Chromosomal inversions are an ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation. We demonstrate that each inversion has a significant effect on transcript abundance for hundreds of genes across the genome. Inversion affected loci (IAL) appear both within inversions as well as on unlinked chromosomes. Importantly, IAL do not appear to be influenced by the previously reported genome-wide expression correlation structure. We found that five genes involved with sterol uptake, four of which are Niemann-Pick Type 2 orthologs, are upregulated in flies with In(3R)Mo but do not have SNPs in LD with the inversion. We speculate that this upregulation is driven by genetic variation in mod(mdg4) that is in LD with In(3R)Mo. We find that there is little evidence for regional or position effect of inversions on gene expression at the chromosomal level but do find evidence for the distal breakpoint of In(3R)Mo interrupting one gene and possibly disassociating the two flanking genes from regulatory elements.

genomics↗