Tree House Explorer: A Novel Genome Browser for Phylogenomics

Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations, recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.

Characterization, Comparison of Four New Mitogenomes of Centrotinae (Hemiptera: Membracidae) and Phylogenetic Implications Supports New Synonymy

To explore the phylogenetic relationships of the subfamily Centrotinae from the mitochondrial genome data, four complete mitogenomes (Anchon lineatus, Anchon yunnanensis, Gargara genistae and Tricentrus longivalvulatus) were sequenced and analyzed. All the newly sequenced mitogenomes contain 37 genes. Among the 13 protein-coding genes (PCGs) of the Centrotinae mitogenomes, a sliding window analysis and the ratio of Ka/Ks suggest that atp8 is a relatively fast evolving gene, while cox1 is the slowest. All PCGs start with ATN, except for nad5 (start with TTG), and stop with TAA or the incomplete stop codon T, except for nad2 and cytb (terminate with TAG). All tRNAs can fold into the typical cloverleaf secondary structure, except for trnS1, which lacks the dihydrouridine (DHU) arm. The BI and ML phylogenetic analyses of concatenated alignments of 13 mitochondrial PCGs among the major lineages produce a well-resolved framework. Phylogenetic analyses show that Membracoidea, Smiliinae and Centrotinae, together with tribes Centrotypini and Leptobelini are recovered as well-supported monophyletic groups. The tribe Gargarini (sensu Wallace et al.) and its monophyly are supported.

Airborne SAR Radiometric Calibration Based on Improved Sliding Window Integral Method

To verify the performance of the high-resolution fully polarimetric synthetic aperture radar (SAR) sensor carried by the Xinzhou 60 remote-sensing aircraft, we used corner reflectors to calibrate the acquired data. The target mechanism in high-resolution SAR images is more complex than it is in low-resolution SAR images, the impact of the point target pointing error on the calibration results is more obvious, and the target echo signal of high-resolution images is more easily affected by speckle noise; thus, more accurate extraction of the point target position and the response energy is required. To solve this problem, this paper introduces image context information and proposes a method to precisely determine the integration region of the corner reflector using sliding windows based on the integral method. The validation indicates that the fully polarimetric SAR sensor on the Xinzhou 60 remote-sensing aircraft can accurately reflect the radiometric characteristics of the ground features and that the integral method can obtain more stable results than the peak method. The sliding window allows the position of the point target to be determined more accurately, and the response energy extracted from the image via the integral method is closer to the theoretical value, which means that the high-resolution SAR system can achieve a higher radiometric calibration accuracy. Additionally, cross-validation reveals that the airborne SAR images have similar quality levels to Sentinel-1A and Gaofen-3 images.