The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig (F. carica)

Abstract

SummaryFicus erecta, a wild relative of the common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programmes. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig. However, this process is time consuming and labour intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programmes. The genome sequence of F. erecta was determined using single‐molecule real‐time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51 806 high‐confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double‐digest restriction‐site‐associated DNA sequencing. Subsequent linkage analysis and whole‐genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome‐wide genotyping analysis enabled the selection of female lines that possessed resistance and effective elimination of the donor genome from the progeny. The genome resources provided in this study will accelerate and enhance disease‐resistance breeding programmes in fig.

Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea)

“…, 2014b; Shirasawa et al. , 2020), whereas M. alba and ramie plants contained 14 chromosomes (Jiao et al. , 2020).…”

The complete plastid genome of Ficus erecta (Moraceae)

“…In this study, we downloaded total 3.9 G data of highquality reads (NCBI accession # DRR187744) using the fastqdump software, which was released by the F. erecta genome sequencing project (Shirasawa et al 2019). The individual for sequencing was a male F. erecta tree "FE-Hiroshima-1" which was grown naturally in Higashi-Hiroshima city in Japan.…”

“…erecta genome sequencing project (Shirasawa et al. 2019 ). The individual for sequencing was a male F .…”

Analysis of the Segregation Distortion of FcRAN1 Genotypes Based on Whole-Genome Resequencing of Fig (Ficus carica L.) Breeding Parents

“…Sequences were obtained using the HiSeq 2000 system in the paired-end mode, with a read length of 151 bp. The generated data were processed as described by Shirasawa et al (2020) . High-quality reads were selected by trimming adapters with fastx_clipper (parameter: -a AGATCGGAAGAGC) in the FASTX Toolkit (version 0.0.13) 1 and deleting low-quality bases with PRINSEQ (version 0.20.4) ( Schmieder and Edwards, 2011 ).…”

“…The SNP effects were categorized using SnpEff (version 3.0) The default parameters of SnpEff were used to analyze variant effects ( Cingolani et al, 2012 ). Genes were predicted and annotated according to previousinformation ( Shirasawa et al, 2020 ).…”