The Ficus erecta genome to identify the Ceratocystis canker resistance gene for breeding programs in common fig (F. carica)

Abstract

<jats:title>Abstract</jats:title><jats:p><jats:italic>Ficus erecta</jats:italic>, a wild relative of common fig (<jats:italic>F. carica</jats:italic>), is a donor of Ceratocystis canker resistance in fig breeding programs. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig; however, this is time consuming and labor-intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for <jats:italic>F. erecta</jats:italic> to facilitate fig breeding programs. The genome sequence of <jats:italic>F. erecta</jats:italic> 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 <jats:italic>F. erecta</jats:italic> 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 selection of female lines that possessed resistance and effective elimination of donor genome from progeny. The genome resources provided in this study will accelerate and enhance disease resistance breeding programs in fig.</jats:p>

A new P450 involved in the furanocoumarin pathway underlies a recent case of convergent evolution

“…Putative marmesin synthases (MSs) are in light blue, others are in light purple. (b) Genomic organization of the F. carica (Usai et al ., 2020) and F. erecta (Shirasawa et al ., 2019) sequences along the chromosomes. The (pseudo)genes are depicted with triangular arrows which direction reflect the gene orientation.…”

“…Genomic analysis showed that all 14 CYP76F sequences from F. carica (Usai et al ., 2020) were clustered on chromosome 11, except one sequence localized on chromosome 2. Similarly, the 16 CYP76Fs from F. erecta (Shirasawa et al ., 2019) were clustered on chromosomes 10 (14 sequences) and 9 (two sequences) (Fig. 4).…”

“…Similarly, the docking results also suggested that the individual mutations of the residues M117 or S305 might be enough to impact the positioning of the DMS within CYP76F112-M117W and CYP76F112-S305P, while the residues T102 and S105 probably both have to be modified (CYP76F112-T102P, S105A) to impact it (Figs 7, S13; Table S4). (Usai et al, 2020) and F. erecta (Shirasawa et al, 2019) sequences along the chromosomes. The (pseudo)genes are depicted with triangular arrows which direction reflect the gene orientation.…”

Breeding Innovations in Underutilized Temperate Fruit Trees

“…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).…”