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

Cui, Ya; Cui, Zhe; Xu, Jianfeng; Hao, Dapeng; Shi, Jiejun; Wang, Dan; Xiao, Hui; Duan, Xiaohong; Chen, Runsheng; Li, Wei

doi:10.1093/nargab/lqaa069

Cited by 9 publications

(5 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Samtools v1.9 (Danecek et al., 2021) was used to extract the coverage per base, including positions with zero depth, from the bam file. The resulting average depth was summarized in overlapping windows of 200 kbp every 100 kbp and visualized using NG‐circos (Cui et al., 2020). In addition, sequences of the 45S rDNA intergenic spacer, 5S rDNA, 45S rDNA, telomeric repeat and TGR1‐4 were searched in MbTMV using blastn and counted in non‐overlapping windows of size 1 Mbp.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

View full text Add to dashboard Cite

SUMMARY 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.

show abstract

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Using the S. baicalensis genome database, chromosome distribution data for R2R3-SbMYB genes was retrieved, and the chromosome position map was generated by Tbtools software [ 63 ]. We examined gene duplication events using the Multiple Collinear Scanning Toolkit (MCScanX) [ 64 ], which was visualized by Circos software [ 65 ]. Syntenic analysis maps were generated using Dual Synteny Plotter software ( , accessed on 12 August 2022) [ 63 ] for investigating the synteny relationships among R2R3-MYBs in S. baicalensis and other species ( A. thaliana , O. sativa , Z. mays , S .…”

Section: Methodsmentioning

confidence: 99%

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

Wang

Zhang

et al. 2022

IJMS

View full text Add to dashboard Cite

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.

show abstract

“…Samtools v1.9 (Danecek et al, 2021) was used to extract the coverage per base, including positions with zero depth, from the bam file. The resulting average depth was summarized in overlapping windows of 200 kbp every 100 kbp and visualized using NGcircos (Cui et al, 2020). In addition, sequences of the 45S rDNA intergenic spacer, 5S rDNA, 45S rDNA, telomeric repeat and TGR1-4 were searched in MbTMV using blastn and counted in non-overlapping windows of size 1 Mbp.…”

Section: Validation Of Mbtmv Assembly By Re-mapping Raw Data and Circos Plotmentioning

confidence: 99%

A gap-free tomato genome built from complementary PacBio and Nanopore long DNA sequences reveals extensive linkage drag during breeding

Rengs

Schmidt

Effgen

et al. 2021

Preprint

View full text Add to dashboard Cite

The assembly and scaffolding of plant crop genomes facilitates the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato 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 merged the HiFi and ONT assemblies to generate a long-read-only assembly where all twelve chromosomes were represented as twelve contiguous sequences (N50=68.5 Mbp). The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato assemblies that made use of genetic maps and HiC 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. 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.

show abstract

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

Cited by 9 publications

References 25 publications

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

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

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

A gap-free tomato genome built from complementary PacBio and Nanopore long DNA sequences reveals extensive linkage drag during breeding

Contact Info

Product

Resources

About