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Biology subjects

Yu, W.-B.

Publications and source records attributed to Yu, W.-B..

2 recordsLinked to original sources

Harnessing historical collections to reconstruct the invasion history of Microstegium vimineum (Poaceae)

The evolutionary processes underlying successful invasions are often difficult to disentangle. Historical collections provide a temporal perspective, offering great potential to reconstruct invasion histories and identify the processes driving invasions. Japanese stiltgrass (Microstegium vimineum) is an invasive C4 grass introduced to eastern North America over a century ago and now established in 31 USA states. To reconstruct its invasion history, we leveraged low-coverage whole-genome sequencing of 142 herbarium and 330 contemporary samples spanning the temporal and spatial extent of the North American invasion and the native range in Asia. We identified three independent introductions in the USA: an awnless form in the South and two independent introductions of awned forms in the North, with limited admixture among introductions across space and time. In both regions, we observed high genetic diversity in the earliest available collections despite demographic bottlenecks and identified several putative selective sweeps in or near flowering-time genes, suggesting rapid evolution in the introduced range. Our analyses support separate invasions in the USA, likely facilitated by standing genetic variation and selection, but provide little support for admixture playing a major role. Our study highlights the power of historical collections to uncover the processes and mechanisms underlying successful biological invasions.

evolutionary biology↗

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↗