Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.)

Calmodulin (CaM) is considered as the most significant Ca²⁺ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.

Galactic Circos: User-friendly Circos plots within the Galaxy platform

BACKGROUND

Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the field of genomic analysis, Circos enables interactive graphing of any analytical data, including alternative scientific domain data and non-scientific data. This high degree of flexibility also comes with a high degree of complexity, which may present an obstacle for researchers not trained in programming or the UNIX command line. The Galaxy platform provides a user-friendly browser-based graphical interface incorporating a broad range of "wrapped" command line tools to facilitate accessibility.

FINDINGS

We have developed a Galaxy wrapper for Circos, thus combining the power of Circos with the accessibility and ease of use of the Galaxy platform. The combination substantially simplifies the specification and configuration of Circos plots for end users while retaining the power to produce publication-quality visualizations of complex multidimensional datasets.

CONCLUSIONS

Galactic Circos enables the creation of publication-ready Circos plots using only a web browser, via the Galaxy platform. Users may download the full set of Circos configuration files of their plots for further manual customization. This version of Circos is available as an open-source installable application from the Galaxy ToolShed, with its use clarified in a training manual hosted by the Galaxy Training Network.

Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era

After human genome sequencing and rapid changes in genome sequencing methods, we have entered into the era of rapidly accumulating genome-sequencing data. This has derived the development of several types of methods for representing results of genome sequencing data. Circular genome visual-ization tools are also critical in this area as they provide rapid interpretation and simple visualization of overall data. In the last 15 years, we have seen rapid changes in circular visualization tools after the de-velopment of the circos tool with 1-2 tools published per year. Herein we have summarized and revisited all these tools until the third quarter of 2018.

CPAP: Cancer Panel Analysis Pipeline

Targeted sequencing using next-generation sequencing technologies is currently being rapidly adopted for clinical sequencing and cancer marker tests. However, no existing bioinformatics tool is available for the analysis and visualization of multiple targeted sequencing datasets. In the present study, we use cancer panel targeted sequencing datasets generated by the Life Technologies Ion Personal Genome Machine Sequencer as an example to illustrate how to develop an automated pipeline for the comparative analyses of multiple datasets. Cancer Panel Analysis Pipeline (CPAP) uses standard output files from variant calling software to generate a distribution map of SNPs among all of the samples in a circular diagram generated by Circos. The diagram is hyperlinked to a dynamic HTML table that allows the users to identify target SNPs by using different filters. CPAP also integrates additional information about the identified SNPs by linking to an integrated SQL database compiled from SNP-related databases, including dbSNP, 1000 Genomes Project, COSMIC, and dbNSFP. CPAP only takes 17 min to complete a comparative analysis of 500 datasets. CPAP not only provides an automated platform for the analysis of multiple cancer panel datasets but can also serve as a model for any customized targeted sequencing project.