Biology subjects

Yim, W. C.

Publications and source records attributed to Yim, W. C..

5 recordsLinked to original sources

bioRxiv2024

Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition

Polyploidization has been recognized as a major force in plant evolution. With the continuous progress in sequencing technologies and genome assembly algorithms, high-quality chromosome-level assemblies of polyploid genomes have become increasingly attainable. However, accurately delineating these assemblies into subgenomes remains a challenging task, especially in case where known diploid ancestors are absent. In this study, we introduce a novel approach that leverages long terminal repeat retrotransposons (LTR-RTs) coupled with the Serial Similarity Matrix (SSM) method to assign genome assemblies to subgenomes, particularly beneficial for those without known diploid progenitor genomes. The SSM method helps identify subgenome-specific LTRs and facilitates the inference of the timing of allopolyploidization events. We validated the efficacy of the SSM approach using well-studied allopolyploidy genomes, Eragrostis tef and Gossypium hirsutum, alongside an artificially created allotetraploid genome by merging two closely related diploid species, Glycine max and G. soja. Our results demonstrated the robustness of the method and its effectiveness in assigning chromosomes to subgenomes. We then applied the SSM method to the octoploid strawberry genome. Our analysis revealed three allopolyploidization events in the evolutionary trajectory of the octoploid strawberry genome, shedding light on the evolutionary process of the origin of the octoploid strawberry genome and enhancing our understanding of allopolyploidization in this complex species.

bioinformatics↗

bioRxiv2024

Proteome-wide neuropeptide identification using NeuroPeptide-HMMer (NP-HMMer)

Neuropeptides are essential neuronal signaling molecules that orchestrate animal behavior and physiology via actions within the nervous system and on peripheral tissues. Due to the small size of biologically active mature peptides, their identification on a proteome-wide scale poses a significant challenge using existing bioinformatics tools like BLAST. To address this, we have developed NeuroPeptide-HMMer (NP-HMMer), a hidden Markov model (HMM)-based tool to facilitate neuropeptide discovery, especially in underexplored invertebrates. NP-HMMer utilizes manually curated HMMs for 46 neuropeptide families, enabling rapid and accurate identification of neuropeptides. Validation of NP-HMMer on Drosophila melanogaster, Daphnia pulex, Tribolium castaneum and Tenebrio molitor demonstrated its effectiveness in identifying known neuropeptides across diverse arthropods. Additionally, we showcase the utility of NP-HMMer by discovering novel neuropeptides in Priapulida and Rotifera, identifying 22 and 19 new peptides, respectively. This tool represents a significant advancement in neuropeptide research, offering a robust method for annotating neuropeptides across diverse proteomes and providing insights into the evolutionary conservation of neuropeptide signaling pathways.

evolutionary biology↗

bioRxiv2022

Evolutionary blocks to anthocyanin accumulation and the loss of an anthocyanin carrier protein in betalain-pigmented Caryophyllales

{square} The order Caryophyllales exhibits complex pigment evolution, with mutual exclusion of anthocyanin and betalain pigments. Given recent evidence for multiple shifts to betalain pigmentation, we re-evaluated potential mechanisms underpinning the exclusion of anthocyanins from betalain-pigmented lineages. {square}We examined the evolution of the flavonoid pathway using transcriptomic and genomic datasets covering 309 species in 31 families. Orthologs and paralogs of known flavonoid synthesis genes were identified by sequence similarity, with gene duplication and gene loss inferred by phylogenetic and syntenic analysis. Relative transcript abundances were assessed to reveal broad-scale gene expression changes between betalain- and anthocyanin-pigmented lineages. {square}Most flavonoid genes are retained and transcribed in betalain-pigmented lineages, and many also show evidence of extensive gene duplication within betalain-pigmented lineages. However, expression of several flavonoid genes is reduced in betalain-pigmented lineages, especially the late-stage genes dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS). Notably flavonoid 3',5'-hydroxylase (F3'5'H) homologs have been repeatedly lost in belatain-pigmented lineages, and Anthocyanin9 (AN9) homologs are undetectable in any betalain-pigmented lineages. {square}Down-regulation of ANS and DFR homolog expression (limiting synthesis) and reiterative loss of AN9 homologs (limiting transport), coincident with multiple shifts to betalain pigmentation, are likely crucial the loss of anthocyanins in betalain-pigmented Caryophyllales.

evolutionary biology↗

bioRxiv2022

The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with significant potential for expanded cultivation as a biodiesel feedstock. The remarkable stress resilience of B. carinata and desirable seed fatty acid profile addresses the ongoing food vs. fuel debate as the crop is productive on marginal lands otherwise not suitable for even closely related species. B. carinata is one of six key Brassica spp. that share three major genomes: three diploid species (AA, BB, CC) that spontaneously hybridized in a pairwise manner, forming three allotetraploid species (AABB, AACC, and BBCC). Each of these genomes has been researched extensively, except for that of B. carinata. In the present study, we report a high-quality, 1.31 Gbp genome with 156.9-fold sequencing coverage for B. carinata var. Gomenzer, completing and confirming the classic Triangle of U, a theory of the evolutionary relationships among these six species that arose almost a century ago. Our assembly provides insights into the genomic features that give rise to B. carinatas superior agronomic traits for developing more climate-resilient Brassica crops with excellent oil production. Notably, we identified an expansion of transcription factor networks and agronomically-important gene families. Completing the Triangle of U comparative genomics platform allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in domestication and agronomical improvement.

genetics↗

bioRxiv2019

Disentangling Sources of Gene Tree Discordance in Phylotranscriptomic Datasets: A Case Study from Amaranthaceae s.l.

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The dataset included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.

evolutionary biology↗