A chromosome‐level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation

Xu, Liang; Wang, Yan; Dong, Junhui; Zhang, Wei; Tang, Mingjia; Zhang, Weilan; Wang, Kai; Chen, Yinglong; Zhang, Xiaoli; He, Qing; Zhang, Xinyu; Wang, Kai; Wang, Lun; Ma, Yinbo; Xia, Kai; Liu, Liwang

doi:10.1111/pbi.14011

Cited by 24 publications

(17 citation statements)

References 90 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To date, radish genome sequencing has previously been carried out for several Asian and European cultivars and isolates [16,17,[27][28][29][30]. The Rs1.0 genome, which is a radish reference genome, was based on the chromosome sequences of R. sativus of the Korean cultivar WK10039 [16].…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Kuznetsova,

Dodueva,

Afonin

et al. 2024

Preprint

View full text Add to dashboard Cite

Spontaneous tumours in higher plants can develop depending on plant genotype without any pathogen invasion. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this work, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We have identified numerous single nucleotide variants (amino acid substitutions, insertions or deletions) that are likely to be associated with the spontaneous tumour formation. Furthermore, we performed the identification of CLE and WOX genes the genomic sequences of the radish inbred lines and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

show abstract

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Kuznetsova,

Dodueva,

Afonin

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…To date, radish genome sequencing has previously been performed for several Asian and European cultivars and isolates [ 16 , 17 , 27 , 28 , 29 , 30 , 31 ]. Polymorphism in radish is being actively studied [ 32 , 33 ].…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Kuznetsova,

Dodueva,

Afonin

et al. 2024

IJMS

View full text Add to dashboard Cite

Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

show abstract

“…A high‐quality genome assembly is crucial for comprehending the genetic basis of economically important traits and enabling molecular breeding in plants (Xu et al ., 2023). In recent years, two V. unguiculata genomes have been assembled, however, numerous sequences remained unassembled or unplaced (Lonardi et al ., 2019; Xia et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

A near‐complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods

Yang,

Wu,

et al. 2023

Plant Biotechnology Journal

View full text Add to dashboard Cite

SummaryAsparagus bean (Vigna unguiculata ssp. sesquipedialis), a subspecies of V. unguiculata, is a vital legume crop widely cultivated in Asia for its tender pods consumed as vegetables. However, the existing asparagus bean assemblies still contain numerous gaps and unanchored sequences, which presents challenges to functional genomics research. Here, we present an improved reference genome sequence of an elite asparagus bean variety, Fengchan 6, achieved through the integration of nanopore ultra‐long reads, PacBio high‐fidelity reads, and Hi‐C technology. The improved assembly is 521.3 Mb in length and demonstrates several enhancements, including a higher N50 length (46.4 Mb), an anchor ratio of 99.8%, and the presence of only one gap. Furthermore, we successfully assembled 14 telomeres and all 11 centromeres, including four telomere‐to‐telomere chromosomes. Remarkably, the centromeric regions cover a total length of 38.1 Mb, providing valuable insights into the complex architecture of centromeres. Among the 30 594 predicted protein‐coding genes, we identified 2356 genes that are tandemly duplicated in segmental duplication regions. These findings have implications for defence responses and may contribute to evolutionary processes. By utilizing the reference genome, we were able to effectively identify the presence of the gene VuMYB114, which regulates the accumulation of anthocyanins, thereby controlling the purple coloration of the pods. This discovery holds significant implications for understanding the underlying mechanisms of color determination and the breeding process. Overall, the highly improved reference genome serves as crucial resource and lays a solid foundation for asparagus bean genomic studies and genetic improvement efforts.

show abstract

A chromosome‐level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation

Cited by 24 publications

References 90 publications

Whole Genome Sequencing and Analysis of Tumour-Forming Radish (<em>Raphanus sativus</em> L.) Line

Whole Genome Sequencing and Analysis of Tumour-Forming Radish (<em>Raphanus sativus</em> L.) Line

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

A near‐complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods

Contact Info

Product

Resources

About