Biology subjects

DeSalle, R.

Publications and source records attributed to DeSalle, R..

3 recordsLinked to original sources

bioRxiv2025

The patchy distribution of the photosynthetic gene cluster in Erythrobacteraceae

The photosynthetic gene cluster which encodes the ability to engage in aerobic anoxygenic photosynthesis is found in multiple clades of Erythrobacteraceae, but whether this patchy distribution was caused by horizontal operon transfer, secondary loss, or a mixed regime of transfer and loss has not previously been answered. We use whole genome sequencing and comparative genomic and phylogenetic methods to address these questions. Two new genomes for Erythrobacteraceae spp. isolates, Altererythrobacter sp. DSM 24483 and Erythrobacter sp. DSM 25594, were sequenced, assembled, and annotated. Despite their disparate sampling locations, these genomes are found to be highly similar, differing chiefly in the presence of four genomic islands unique to DSM 24483. A species phylogeny for 91 members of Erythrobacteraceae, including the two new genomes, was generated from whole genome data, expanding the most recently published phylogeny for this family by 17 species. Results of the phylogenetic analysis indicate that all species which both possess the photosynthetic gene cluster and express bacteriochlorophyll a in culture form one clade, corresponding to the Erythrobacter genus. Finally, two hypotheses about the evolution of phototrophy in Erythrobacteraceae are tested. Two methods of ancestral state reconstruction and gene order data are leveraged to determine whether secondary loss, horizontal operon transfer, or a mixed regime of transfer and loss explains the patchy distribution of the photosynthetic gene cluster in Erythrobacteraceae. Horizontal operon transfer is found to be the best explanation for the evolution of the patchy distribution of the photosynthetic gene cluster in Erythrobacteraceae.

evolutionary biology↗

bioRxiv2021

What do we gain when tolerating loss? The information bottleneck, lossy compression, and detecting horizontal gene transfer

Most microbes have the capacity to acquire genetic material from their environment. Recombination of foreign DNA yields genomes that are, at least in part, incongruent with the vertical history of their species. Dominant approaches for detecting these transfers are phylogenetic, requiring a painstaking series of analyses including alignment and phylogenetic tree reconstruction. These traditional pan-genomic methods do not scale. Here we propose an unsupervised, alignment-free and tree-free technique based on the sequential information bottleneck (SIB), an optimization procedure designed to extract some portion of relevant information from one random variable conditioned on another. In our case, this joint probability distribution tabulates occurrence counts of k-mers against their genomes of origin with the expectation that recombination will create a strong signal that unifies certain sets of co-occuring k-mers. We conceptualize the technique as a rate-distortion problem, measuring distortion in the relevance information as k-mers are compressed into clusters based on their co-occurrence in the source genomes. The result is fast, model-free, lossy compression of k-mers into groups that learns tracts of shared genome sequence differentiating recombined elements from the vertically inherited core. We show that the technique yields a new recombination measure based purely on information, divorced from any biases and limitations inherent to alignment and phylogeny. SignificanceThe information bottleneck, a lossy compression technique borrowed from the information theoretic and Natural Langauge Processing literature, is well suited to detecting evolutionary patterns in sets of co-occuring k-mers. Here we show that we can detect simulated and real recombination events while highlighting a core set of k-mers that comprise the vertically inherited portion of any set of genomes. Moreover, the compressibility of any given set of genomes offers a new way to compare the pangenomes of clades across the microbial tree of life. In our application, the bottleneck is informed by genome origin, our relevance variable, but the technique is general. The information bottleneck can be used for any biological contingency matrix where the goal is to learn groups from unstructured data.

evolutionary biology↗

bioRxiv2019

Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata

The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin A. mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, while A. mellifera nest in concealed cavities. Additionally, the worker and reproductive castes are all of the same size in A. dorsata. In order to investigate these differences, we performed whole genome sequencing of A. dorsata using a hybrid Oxford Nanopore and Illumina approach. The 223MB genome has an N50 of 35kb with the largest scaffold of 302kb. We have found that there are many genes in the dorsata genome that are distinct from other hymenoptera and also large amounts of transposable elements, and we suggest some candidate genes for A. dorsatas exceptional level of defensive aggression.

genomics↗