Biology subjects

Seah, Y. M.

Publications and source records attributed to Seah, Y. M..

3 recordsLinked to original sources

bioRxiv2025

Begomovirus species demarcation based on genome-sequence identity often yields non-monophyletic species: A case study of sweet potato-infecting begomoviruses

Sweepoviruses are single stranded DNA viruses in the genus Begomovirus which infect sweet potato (Ipomoea batatas). The Geminiviridae and Tolecusatellitidae study group of the International Committee for the Taxonomy of Viruses (ICTV) specifies a percent nucleotide identity threshold for species demarcation, but these criteria have not been systematically applied across sweepoviruses. Simultaneously, ICTV aims for species to be monophyletic. A maximum likelihood phylogeny of 398 full genome sequences of sweepoviruses only supported the monophyly of four of 14 ICTV-recognized species. Another species has a well-supported paraphyly, which is a legitimate biological possibility for these viruses. These analyses revealed a distinct difference in isolates of the sweet potato leaf curl Hubei virus (Begomovirus ipomoeahubeiense) versus isolates of all other species, a result substantiated by previous findings that this species is the product of recombination with a non-sweepovirus begomovirus. We found extensive recombination among the sweepoviruses, including across species boundaries, which is at odds with the goal of monophyletic species. Reclassifying the current sequences of sweepoviruses under the ICTV-specified species delineation would cut the number of sweepovirus species in half, and only five of these seven species could be considered monophyletic. Our analyses highlight the failure of a percent nucleotide identity threshold to create monophyletic species. The particularly low threshold for novel species in Begomovirus also conflates lineages that are mostly separately evolving into a single species, leading to average percent nucleotide identities within species that are less than the threshold for being members of the same species (<91%).

evolutionary biology↗

bioRxiv2022

Identifying indels from WGS short reads of haploid genomes distinguishes variant-calling algorithms

Identification of clinically relevant strains of bacteria increasingly relies on whole genome sequencing. The downstream bioinformatics steps necessary for calling variants from short read sequences are well-established but seldom validated against haploid genomes. We devised an in silico workflow to introduce single nucleotide polymorphisms (SNP) and indels into bacterial reference genomes, and computationally generate sequencing reads based on the mutated genomes. We then applied the method to Mycobacterium tuberculosis H37Rv and used the synthetic reads as truth sets for evaluating several popular variant callers. Insertions proved especially challenging for most variant callers to correctly identify, relative to deletions and single nucleotide polymorphisms. With adequate read depth, however, variant callers that use high quality soft-clipped reads and base mismatches to perform local realignment consistently had the highest precision and recall in identifying medium-length insertions and deletions.

bioinformatics↗

bioRxiv2020

Synergistic epistasis enhances cooperativity of mutualistic interspecies interactions

Frequent fluctuations in sulfate availability rendered syntrophic interactions between the sulfate reducing bacterium Desulfovibrio vulgaris (Dv) and the methanogenic archaeon Methanococcus maripaludis (Mm) unsustainable. By contrast, prolonged laboratory evolution in obligate syntrophy conditions improved the productivity of this community but at the expense of erosion of sulfate respiration (SR). Hence, we sought to understand the evolutionary trajectories that could both increase the productivity of syntrophic interactions and sustain SR. We combined a temporal and combinatorial survey of mutations accumulated over 1000 generations of 9 independently-evolved communities with analysis of the genotypic structure for one community down to the single-cell level. We discovered a high level of parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance of a rare SR+ Dv lineage within many evolution lines. An in-depth investigation revealed that synergistic epistasis across Dv and Mm genotypes had enhanced cooperativity within SR- and SR+ assemblages, allowing their co-existence as r- and K-strategists, respectively.

evolutionary biology↗