Biology subjects

Choi, J. Y.

Publications and source records attributed to Choi, J. Y..

5 recordsLinked to original sources

bioRxiv2018

Evolutionary rate covariation analysis of E-cadherin identifies Raskol as regulator of cell adhesion and actin dynamics in Drosophila

The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization. The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link cortical actin to intercellular adhesions. Over time, evolutionary pressures have shaped the signaling and mechanical functions of the adherens junction to meet specific developmental and physiological demands. Evolutionary rate covariation (ERC) identifies genes with correlated fluctuations in evolutionary rate that can reflect shared selective pressures and functions. Here we use ERC to identify genes with evolutionary histories similar to shotgun (shg), which encodes the Drosophila E-cadherin (DE-Cad) ortholog. Core adherens junction components -catenin and p120-catenin displayed strong ERC correlations with shg, indicating that they evolved under similar selective pressures during evolution between Drosophila species. Further analysis of the shg ERC profile revealed a collection of genes not previously associated with shg function or cadherin-mediated adhesion. We then analyzed the function of a subset of ERC-identified candidate genes by RNAi during border cell (BC) migration and identified novel genes that function to regulate DE-Cad. Among these, we found that the gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates BC migration and adhesion. We named CG42684 raskol (\"to split\" in Russian) and show that it regulates DE-Cad levels and actin protrusions in BCs. We propose that Raskol functions with DE-Cad to restrict Ras/Rho signaling and help guide BC migration. Our results demonstrate that a coordinated selective pressure has shaped the adherens junction and this can be leveraged to identify novel components of the complexes and signaling pathways that regulate cadherin-mediated adhesion.\n\nAuthor SummaryThe establishment of intercellular adhesions facilitated the genesis of multicellular organisms. The adherens junction, which links the actin cytoskeletons of neighboring cells, arose early in the evolution of multicellularity and selective pressures have shaped its function and molecular composition over time. In this study, we used evolutionary rate covariation (ERC) analysis to examine the evolutionary history of the adherens junction and to identify genes that coevolved with the adherens junction gene shotgun, which encodes the Drosophila E-cadherin (DE-Cad). ERC analysis of shotgun revealed a collection of genes with similar evolutionary histories. We then tested the role of these genes in border cell migration in the fly egg chamber, a process that requires the coordinated regulation of cell-cell adhesion and cell motility. Among these, we found that a previously uncharacterized gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates the collective cell migration of border cells, stabilizes cell-cell adhesions and regulates the actin dynamics. Our results demonstrate that components of the adherens junction share an evolutionary history and that ERC analysis is a powerful method to identify novel components of cell adhesion complexes in Drosophila.

genetics↗

bioRxiv2018

Nanopore sequence-based genome assembly of the basmati rice

BACKGROUNDThe circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the groups evolutionary history is not fully resolved. To address these gaps, we used long-read nanopore sequencing and assembled the genomes of two circum-basmati rice varieties, Basmati 334 and Dom Sufid.\n\nRESULTSWe generated two high-quality, chromosome-level reference genomes that represented the 12 chromosomes of Oryza. The assemblies showed a contig N50 of 6.32Mb and 10.53Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies we characterized structural variations segregating across circum-basmati genomes. We discovered repeat expansions not observed in japonica--the rice group most closely related to circum- basmati--as well as presence/absence variants of over 20Mb, one of which was a circum- basmati-specific deletion of a gene regulating awn length. We further detected strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow had its greatest effect on chromosome 10, causing both structural variation and single nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties showed three major geographically structured genetic groups: (1) Bhutan/Nepal group, (2) India/Bangladesh/Myanmar group, and (3) Iran/Pakistan group.\n\nCONCLUSIONAvailability of high-quality reference genomes from nanopore sequencing allowed functional and evolutionary genomic analyses, providing genome-wide evidence for gene flow between circum-aus and circum-basmati, the nature of circum-basmati structural variation, and the presence/absence of genes in this important and iconic rice variety group.

evolutionary biology↗

bioRxiv2018

Impact of Chronic Total Occlusion Lesion Length onSix-month Angiographic and 2-year Clinical Outcomes

BackgroundSuccessful chronic total occlusion (CTO) percutaneous coronary intervention (PCI) is known to be associated with improved clinical outcomes compared with failed CTO PCI. However, it is not clear whether the angiographic and clinical outcomes of long CTO lesionis different with those of short CTO lesion in the drug eluting stent (DES) era.\n\nMethod sand ResultsA total of 235 consecutive patients underwent successful CTO intervention were divided into two groups according the CTO lesion length. Six-month angiographic and two-year clinical outcomes were compared between the two groups. The baseline clinical characteristics were similar between the two groups except prior PCI was more frequent in long CTO group whereas bifurcation lesion was more frequent in the short CTO group. In-hospital complications were similar between the two groups except intimal dissection was more frequent in long CTO group. Both groups had similar angiographic outcomes at 6 months and clinical outcomes up to 2 years except the incidence of repeat PCI, predominantly target vessel revascularization (TVR) was higher in long CTO group. In multivariate analysis, long CTO was an important predictor for repeat PCI (OR;4.26, CI 1.53-11.9, p=0.006).\n\nConclusionThe safety profile, angiographic and 2-year clinical outcomes were similar between the two groups except higher incidence of repeat PCI in long CTO group despite of successful PCI with DESs.

physiology↗

bioRxiv2018

The complex geography of domestication of the African rice Oryza glaberrima

While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remains elusive. The inner Niger delta has been suggested as the center of origin but molecular data for its support are lacking. Here, we present the most comprehensive analysis to date on the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals in domesticated African rice Oryza glaberrima and its progenitor O. barthii, we hypothesize a non-centric domestication origin for African rice. Our analyses show geographically based population structure in O. glaberrima, as well as significant evidence of admixture between genetic groups. Furthermore, we have evidence that the previously hypothesized O. barthii progenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors may actually represent feral wild-domesticated hybrid rice. Demography modeling suggested the inland O. glaberrima had a protracted period of bottlenecking that preceded the coastal population by 800-1,800 years. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. Based on our evidence, we hypothesize O. glaberrima was not domesticated from a single centric location but was rather a diffuse process where multiple regions contributed key alleles for different domestication traits.\n\nAuthor SummaryFor many crops it is not clear how they got domesticated from their wild progenitors. Transition from a wild to domesticated state required a series of genetic changes, and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop. Moreover, population relationships within a crop holds insight into the evolutionary history of domestication and whether there was gene flow between different genetic groups. In this study, we investigate the domestication history of Oryza glaberrima, a rice species that was domesticated in West Africa independently from the Asian rice species O. sativa. Using genome-wide data from a large sample of domesticated and wild African rice samples we did not find evidence that supported the established domestication model for O. glaberrima--a single domestication origin. Rather, our evidence suggests the domestication process for African rice was initiated in multiple regions of West Africa, caused potentially by the local environmental and cultivation preference of people. Admixture between different genetic groups had facilitated the exchange and spread of core domestication mutations. Hence domestication of African rice was a multi-regional process.

evolutionary biology↗

bioRxiv2017

Multiple origin but single domestication led to domesticated Asian rice

The domestication scenario that led to Asian rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated rice dataset, which were also analyzed by two studies but resulted in two contrasting domestication models. We suggest the analysis of false positive selective sweep regions and phylogenetic analysis of concatenated genomic regions may have been the sources that contributed to the different results. In the end, our result indicates Asian rice originated from multiple wild progenitor subpopulations; however, de novo domestication appears to have occurred only once and the domestication alleles were transferred between rice subpopulation through introgression.

evolutionary biology↗