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  1. Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it is unknown what underlies the transcriptional divergence of duplicated genes in polyploid species that lack subgenome dominance. Soybean is a paleotetraploid with a WGD that occurred 5 to 13 Mya. Approximately 50% of the duplicated genes retained from this WGD exhibit transcriptional divergence. We developed accessible chromatin region (ACR) datasets from leaf, flower, and seed tissues using MNase-hypersensitivity sequencing. We validated enhancer function of several ACRs associated with known genes using CRISPR/Cas9-mediated genome editing. The ACR datasets were used to examine and correlate the transcriptional patterns of 17,111 pairs of duplicated genes in different tissues. We demonstrate that ACR dynamics are correlated with divergence of both expression level and tissue specificity of individual gene pairs. Gain or loss of flanking ACRs and mutation ofcis-regulatory elements (CREs) within the ACRs can change the balance of the expression level and/or tissue specificity of the duplicated genes. Analysis of DNA sequences associated with ACRs revealed that the extensive sequence rearrangement after the WGD reshaped the CRE landscape, which appears to play a key role in the transcriptional divergence of duplicated genes in soybean. This may represent a general mechanism for transcriptional divergence of duplicated genes in polyploids that lack subgenome dominance.

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    Free, publicly-accessible full text available October 31, 2024
  2. Free, publicly-accessible full text available September 1, 2024
  3. Abstract

    Four statistical selection methods for inferring transcription factor (TF)–target gene (TG) pairs were developed by coupling mean squared error (MSE) or Huber loss function, with elastic net (ENET) or least absolute shrinkage and selection operator (Lasso) penalty. Two methods were also developed for inferring pathway gene regulatory networks (GRNs) by combining Huber or MSE loss function with a network (Net)-based penalty. To solve these regressions, we ameliorated an accelerated proximal gradient descent (APGD) algorithm to optimize parameter selection processes, resulting in an equally effective but much faster algorithm than the commonly used convex optimization solver. The synthetic data generated in a general setting was used to test four TF–TG identification methods, ENET-based methods performed better than Lasso-based methods. Synthetic data generated from two network settings was used to test Huber-Net and MSE-Net, which outperformed all other methods. The TF–TG identification methods were also tested with SND1 and gl3 overexpression transcriptomic data, Huber-ENET and MSE-ENET outperformed all other methods when genome-wide predictions were performed. The TF–TG identification methods fill the gap of lacking a method for genome-wide TG prediction of a TF, and potential for validating ChIP/DAP-seq results, while the two Net-based methods are instrumental for predicting pathway GRNs.

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  4. Free, publicly-accessible full text available October 1, 2024
  5. The increasing wildfire activity and rapid population growth in the wildland–urban interface (WUI) have made more Americans exposed to wildfire risk. WUI mapping plays a significant role in wildfire management. This study used the Microsoft building footprint (MBF) and the Montana address/structure framework datasets to map the WUI in Montana. A systematic comparison of the following three types of WUI was performed: the WUI maps derived from the Montana address/structure framework dataset (WUI-P), the WUI maps derived from the MBF dataset (WUI-S), and the Radeloff WUI map derived from census data (WUI-Z). The results show that WUI-S and WUI-P are greater than WUI-Z in the WUI area. Moreover, WUI-S has more WUI area than WUI-P due to the inclusion of all structures rather than just address points. Spatial analysis revealed clusters of high percentage WUI area in western Montana and low percentage WUI area in eastern Montana, which is likely related to a combination of factors including topography and population density. A web GIS application was also developed to facilitate the dissemination of the resulting WUI maps and allow visual comparison between the three WUI types. This study demonstrated that the MBF can be a useful resource for mapping the WUI and could be used in place of a national address point dataset. 
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