NG-Circos: next-generation Circos for data visualization and interpretation

The first complete mitochondrial genome of Grossulariaceae: Molecular features, structure recombination, and genetic evolution

BACKGROUND

Mitochondria play crucial roles in the growth, development, and adaptation of plants. Blackcurrant (Ribes nigrum L.) stands out as a significant berry species due to its rich nutritional profile, medicinal properties, and health benefits. Despite its importance, the mitochondrial genome of blackcurrant remains unassembled.

RESULTS

This study presents the first assembly of the mitochondrial genome of R. nigrum in the Grossulariaceae family. The genome spans 450,227 base pairs (bp) and encompasses 39 protein-coding genes (PCGs), 19 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). Protein-coding regions constitute 8.88% of the entire genome. Additionally, we identified 180 simple sequence repeats, 12 tandem repeats, and 432 pairs of dispersed repeats. Notably, the dispersed sequence R1 (cotig3, 1,129 bp) mediated genome recombination, resulting in the formation of two major conformations, namely master and double circles. Furthermore, we identified 731 C-to-U RNA editing sites within the PCGs. Among these, cox1-2, nad1-2, and nad4L-2 were associated with the creation of start codons, whereas atp6-718 and rps10-391 were linked to termination codons. We also detected fourteen plastome fragments within the mitogenome, constituting 1.11% of the total length. Phylogenetic analysis suggests that R. nigrum might have undergone multiple genomic reorganization and/or gene transfer events, resulting in the loss of two PCGs (rps2 and rps11) during its evolutionary history.

CONCLUSIONS

This investigation unveils the molecular characteristics of the R. nigrum mitogenome, shedding light on its evolutionary trajectory and phylogenetic implications. Furthermore, it serves as a valuable reference for evolutionary research and germplasm identification within the genus.

shinyCircos-V2.0: Leveraging the creation of Circos plot with enhanced usability and advanced features

We previously developed shinyCircos, an interactive web application for creating Circos diagrams, which has been widely recognized for its graphical user interface and ease of use. Here, we introduce shinyCircos-V2.0, an upgraded version of shinyCircos that includes a new user interface with enhanced usability and many new features for creating advanced Circos plots. To help users get started with shinyCircos-V2.0, we provide detailed tutorials and example input data sets. The application is available online at https://venyao.xyz/shinyCircos/ and https://asiawang.shinyapps.io/shinyCircos/, or can be installed locally using the source code deposited in GitHub (https://github.com/YaoLab-Bioinfo/shinyCircos-V2.0).

A painless way to customize Circos plot: From data preparation to visualization using TBtools

Circos plots enable scientists to easily inspect big biological data genome-widely on a macroscopic scale, but cumbersome preparation of input data and complex parameter configuration limits its application. We have developed the "Advanced Circos" function in TBtools, to provide a simple way to construct Circos plots. As an out-of-the-box combo toolkit, TBtools has integrated a set of functions convenient for input data preparation. The "Advanced Circos" function is supplied with a user-friendly interface for the customization of parameter settings and can be deployed to visualize all kinds of genomic data, such as genomic associations, alignment data, gene density, and QTL locations. In the present article, we introduce the main features of "Advance Circos" and the protocols of upstream data preparation, aiming to endow more users with the ability to use Circos plots in big genomic data exploration.

Systematic Analysis and Functional Characterization of R2R3-MYB Genes in Scutellaria baicalensis Georgi

R2R3-MYB transcription factors participate in multiple critical biological processes, particularly as relates to the regulation of secondary metabolites. The dried root of Scutellaria baicalensis Georgi is a traditional Chinese medicine and possesses various bioactive attributes including anti-inflammation, anti-HIV, and anti-COVID-19 properties due to its flavonoids. In the current study, a total of 95 R2R3-MYB genes were identified in S. baicalensis and classified into 34 subgroups, as supported by similar exon–intron structures and conserved motifs. Among them, 93 R2R3-SbMYBs were mapped onto nine chromosomes. Collinear analysis revealed that segmental duplications were primarily responsible for driving the evolution and expansion of the R2R3-SbMYB gene family. Synteny analyses showed that the ortholog numbers of the R2R3-MYB genes between S. baicalensis and other dicotyledons had a higher proportion compared to that which is found from the monocotyledons. RNA-seq data indicated that the expression patterns of R2R3-SbMYBs in different tissues were different. Quantitative reverse transcriptase-PCR (qRT-PCR) analysis showed that 36 R2R3-SbMYBs from different subgroups exhibited specific expression profiles under various conditions, including hormone stimuli treatments (methyl jasmonate and abscisic acid) and abiotic stresses (drought and cold shock treatments). Further investigation revealed that SbMYB18/32/46/60/70/74 localized in the nucleus, and SbMYB18/32/60/70 possessed transcriptional activation activity, implying their potential roles in the regulatory mechanisms of various biological processes. This study provides a comprehensive understanding of the R2R3-SbMYBs gene family and lays the foundation for further investigation of their biological function.

A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding

The assembly and scaffolding of plant crop genomes facilitate the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato (Solanum lycopersicum) has been improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of tobacco mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT Nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV-resistant tomato variety. We show specific examples of how HiFi and ONT datasets can complement one another to improve assembly contiguity. We merged the HiFi and ONT assemblies to generate a long-read-only assembly where all 12 chromosomes were represented as 12 contiguous sequences (N50 = 68.5 Mbp). This chromosome scale assembly did not require scaffolding using an orthogonal data type. The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato genome assemblies that made use of genetic maps and Hi-C for scaffolding. Our long-read-only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1-Mbp region of the S. peruvianum genome during tomato breeding. Through marker studies and ONT-based comprehensive haplotyping we show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near-complete genome sequences.

interacCircos: an R package based on JavaScript libraries for the generation of interactive Circos plots

SUMMARY

JavaScript-based Circos libraries have been widely implemented to generate interactive Circos plots in web applications. However, these libraries require either local installation, which requires the compilation of extra libraries, or extra data processing procedures to prepare input and configuration for each track of plot, which limits the utility and capability of integration with powerful R packages. In this report, we present interacCircos, an R package for creating interactive Circos plots through the integration of JavaScript-based libraries. interacCircos can simply and flexibly implement 14 track-plot functions and 7 auxiliary functions for presenting large-scale genomic data in interactive Circos plots.

AVAILABILITY AND IMPLEMENTATION

InteracCircos and its manual are freely available at https://github.com/mrcuizhe/interacCircos. The online documentation is available at https://mrcuizhe.github.io/interacCircos_documentation/index.html under the GPL license. We thank the teams of BioCircos.js, BioCircos.R, NGCircos and circosJS for sharing the code.