Biology subjects

Brown, T. A.

Publications and source records attributed to Brown, T. A..

3 recordsLinked to original sources

bioRxiv2018

Comment on ‘Multiple Origin but Single Domestication Led to Oryza sativa’

In 2015, we published an analysis of rice genomic data and showed that the japonica, indica and aus groups of cultivated rice were independently domesticated. Our conclusions were controversial as they contradicted a previous, high-profile analysis of the same dataset, which had suggested that all of cultivated rice derives from a single origin. Although there have been attempts since 2015 to bolster the single-origin hypothesis, until recently there has been no direct rebuttal of the methodology that we used to infer multiple origins. Such a rebuttal has now been published (Choi J.Y., Purugganan M.D., 2018 Multiple origin but single domestication led to Oryza sativa. G3 8:797-803), but the reanalysis that is presented only supports the single origin hypothesis if phylogenetic trees that are clearly paraphyletic are interpreted as monophyletic, and furthermore addresses only one component of the evidence that we presented for multiple domestications. We caution against accepting these analyses uncritically.

evolutionary biology↗

bioRxiv2017

A general method to fine-tune fluorophores for live-cell and in vivo imaging

AO_SCPCAPBSTRACTC_SCPCAPPushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the Janelia Fluor (JF) series of dyes. Here, we refine and extend this strategy, showing that incorporation of 3-substituted azetidine groups allows rational tuning of the spectral and chemical properties with unprecedented precision. This strategy yields a palette of new fluorescent and fluorogenic labels with excitation ranging from blue to the far-red with utility in live cells, tissue, and animals.

cell biology↗

bioRxiv2016

Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.)

Cultivated Asian rice (O. sativa L.) comprises several groups with distinct ecological requirements and culinary uses. While the two subspecies of O. sativa - indica and japonica - have been subjected to a multitude of genetic and genomic analyses, less is known about the origins and diversity of the agronomically marginal groups - aus and aromatic rice. Here we reconstructed complete chloroplast genomes of over 1,800 accessions of wild and cultivated rice, including 240 aus and 73 aromatic varieties, and analysed the haplotype diversity of the taxonomic groups. We confirm the deep phylogenetic divergence between the main chloroplast haplotypes of japonica and indica, and reveal unique profiles of chloroplast diversity in aus and aromatic rice. Our results indicate that the latter two groups are not simple derivatives of indica and japonica, respectively, but originated from independent and/or reticulate domestication processes. Absence of phylogeographic patterns in the wild distribution of chloroplast haplogroups did not allow firm conclusions about geographic origins and the role of inter-group gene flow. Nonetheless, our results suggest that the domestication of indica, japonica, aus and aromatic rice operated on genetically different gene pools and followed different dynamics.

genomics↗