Biology subjects

Yi, T.-S.

Publications and source records attributed to Yi, T.-S..

5 recordsLinked to original sources

bioRxiv2025

Longevity in plants impacts phylogenetic and population dynamics

Many long-lived plant species exhibit notable patterns in phylogenies, such as short molecular branch lengths and high gene-tree conflict. However, it is not clear what biological properties of long-lived plant species or concomitant processes acting within these lineages generate these patterns. To explore this mystery, we implemented an agent-based model and conducted simulations to investigate how longevity affects molecular evolution and population dynamics. Through these simulations, we demonstrated that the patterns exhibited in empirical datasets for long-lived species can be explained by their lifespan and overlapping generations. We also show that somatic mutations can exacerbate these patterns, although evidence for substantive rates in empirical systems high enough to impact phylogenetic patterns is scarce. We discuss several empirical datasets containing life history shifts that exhibit diverse phylogenomic patterns. The variation produced through different parameterizations of our simulations reflects the diversity of patterns found in empirical datasets. Our results have broad implications for phylogenomic patterns and population genetics in general, as well as for specifically explaining patterns of evolution in long-lived lineages.

evolutionary biology↗

bioRxiv2025

PlastidHub: an integrated analysis platform for plastid phylogenomics and comparative genomics

The plastome (plastid genome) represents an indispensable molecular data source for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genome, accurate and efficient annotation and of use plastome sequences are not simple tasks. Therefore, a streamlined phylogenomic pipeline from plastome annotation to phylogenetic reconstruction and comparative genomics would greatly facilitate research using this important organellar genome. Here we develop PlastidHub, a new web application that primarily uses novel tools to analyze plastome sequences. In comparison with existing tools, new functionalities in PlastidHub include: (1) standardization of quadripartite structure; (2) improvement of annotation flexibility and consistency; (3) quantitative assessment of annotation completeness; (4) diverse extraction modes for canonical and specialized sequences; (5) intelligent screening of molecular markers for biodiversity studies; (6) visual comparison of structural variations and annotation completeness at the gene-level. PlastidHub has the following features: cloud-based web applications that do not require users to install, update, or maintain tools; detailed help documents including user guides, test examples, a static pop-up prompt box, and dynamic pop-up warning prompts when entering unreasonable parameter values; batch processing functionalities for all tools; intermediate result documents for secondary use; and easy-to-operate task flows between file upload and download. Interrelated task-based user interface design is the most important feature of PlastidHub. Give that PlastidHub is easy to use without specialized computational skills or resources, this new platform should become widely used among botanists and evolutionary biologists, improving and expediting research employing the plastome. PlastidHub is available at https://www.plastidhub.cn.

plant biology↗

bioRxiv2024

Chromosome-level reference genome assembly for the protected resource plant, Zenia insignis

Zenia insignis Chun, from the subfamily Dialioideae of Fabaceae, is a tree species of significant economic and ecological values. It is a threatened species as per the IUCN Red List. The absence of a reference genome has impeded research on Z. insignis despite its importance. In this study, we generated a reference genome for Z. insig n, iws ith a contig N50 of 6.02Mb, a total length of 361.11 Mb, and 97.71% of the sequences assembled into 14 pseudo-chromosomes. The BUSCO assessment score for completeness is 97.30%, and the LAI index assessment score for continuity is 14.57. To our knowledge, this is the first reported nuclear genome of a species belonging to subfamily Dialioideae. The reference genome will provide a valuable resource for the phylogenomic studies of the Fabaceae family and facilitate further research on Z. insignis.

genomics↗

bioRxiv2021

Gene duplications and genomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the Tree of Life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation1, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here we examine the relationship of various facets of genomic evolution--including gene and genome duplication, genome size, and chromosome number--with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.

evolutionary biology↗

bioRxiv2018

GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data

GetOrganelle is a state-of-the-art toolkit to assemble accurate organelle genomes from NGS data. This toolkit recruit organelle-associated reads using a modified \"baiting and iterative mapping\" approach, conducts de novo assembly, filters and disentangles assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published samples, we reassembled the circular plastome in 47 samples using GetOrganelle, but only in 12 samples using NOVOPlasty. In comparison with published/NOVOPlasty plastomes, we demonstrated that GetOrganelle assemblies are more accurate. Moreover, we assembled complete mitogenomes of fungi and animals using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).

bioinformatics↗