Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)

Mori, Kazuki; Shirasawa, Kenta; Nogata, Hitoshi; Hirata, Chiharu; Tashiro, Kosuke; Habu, Toshiyuki; Kim, Sangwan; Himeno, Shuichi; Kuhara, Satoru; Ikegami, Hiroyasu

doi:10.1038/srep41124

Cited by 60 publications

(119 citation statements)

References 44 publications

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“…In particular, a definitive proof of cospeciation resulting from co‐evolution (e.g., rather than from similar responses to geographic isolation) would require demonstrating a match between the signal genes in figs (scent pathways) and receiver genes in wasps (olfactory receptors; Segar, Volf, Sisol, Pardikes, & Souto‐Vilarós, ). While the genomic data for such analyses are becoming increasingly available (Mori et al, ; Xiao et al, ) they have yet to be compiled for our study system. Genomic matching of the corresponding genes in plants and pollinators stands out as the necessary next step toward the mechanistic understanding of cospeciation patterns (Segar et al, ).…”

Section: Discussionmentioning

confidence: 99%

Faster speciation of fig‐wasps than their host figs leads to decoupled speciation dynamics: Snapshots across the speciation continuum

et al. 2019

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Even though speciation involving multiple interacting partners, such as plants and their pollinators, has attracted much research, most studies focus on isolated phases of the process. This currently precludes an integrated understanding of the mechanisms leading to cospeciation. Here, we examine population genetic structure across six species‐pairs of figs and their pollinating wasps along an elevational gradient in New Guinea. Specifically, we test three hypotheses on the genetic structure within the examined species‐pairs and find that the hypothesized genetic structures represent different phases of a single continuum, from incipient cospeciation to the full formation of new species. Our results also illuminate the mechanisms governing cospeciation, namely that fig wasps tend to accumulate population genetic differences faster than their figs, which initially decouples the speciation dynamics between the two interacting partners and breaks down their one‐to‐one matching. This intermediate phase is followed by genetic divergence of both partners, which may eventually restore the one‐to‐one matching among the fully formed species. Together, these findings integrate current knowledge on the mechanisms operating during different phases of the cospeciation process. They also reveal that the increasingly reported breakdowns in one‐to‐one matching may be an inherent part of the cospeciation process. Mechanistic understanding of this process is needed to explain how the extraordinary diversity of species, especially in the tropics, has emerged. Knowing which breakdowns in species interactions are a natural phase of cospeciation and which may endanger further generation of diversity seems critical in a constantly changing world.

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Section: Discussionmentioning

confidence: 99%

Faster speciation of fig‐wasps than their host figs leads to decoupled speciation dynamics: Snapshots across the speciation continuum

et al. 2019

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“…The sequences were connected with ten thousand of Ns to construct pseudomolecule sequences, namely the FER_r1.1.pseudomolecule dataset. The names and directions of the pseudomolecule sequences were assigned in accordance with the previously described high-density genetic map for fig (Mori et al, 2017). Sequences that were unassigned to the genetic map were connected and termed chromosome 0 (FER_r1.1chr00).…”

Section: Resultsmentioning

confidence: 99%

“…During breeding, therefore, selection of female plants as well as of those exhibiting favorable traits is desirable. Using whole genome sequence analysis, Mori et al (2017) identified a candidate for the fig sex determinant gene, an ortholog of RESPONSIVE-TO-ANTAGONIST1 ( RAN1 ) in Arabidopsis (Hirayama et al, 1999), and developed a DNA marker linked to the locus, allowing identification of female seedlings prior to fruit bearing (Mori et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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

Shirasawa

Yakushiji

Nishimura

et al. 2019

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AbstractFicus erecta, a wild relative of common fig (F. carica), 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 F. erecta to facilitate fig breeding programs. 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 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.

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“…Horaishi [10]. Whilst the vast majority of genes were found in both cultivars, a number of genes were recovered specifically in either the Japanese cultivar or the Italian cultivar (Fig.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 97%

Cultivar-specific transcriptome prediction and annotation in Ficus carica L.

et al. 2017

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The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv. Dottato. Then, putative gene sequences were predicted and annotated. Finally, a comparison was performed between cvs. Dottato and Horaishi predicted transcriptomes. Our data provide a resource (available at the Sequence Read Archive database under SRP109082) to be used for functional genomics of fig, in order to fill the gap of knowledge still existing in this species concerning plant development, defense and adaptation to the environment.

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Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)

Cited by 60 publications

References 44 publications

Faster speciation of fig‐wasps than their host figs leads to decoupled speciation dynamics: Snapshots across the speciation continuum

Faster speciation of fig‐wasps than their host figs leads to decoupled speciation dynamics: Snapshots across the speciation continuum

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

Cultivar-specific transcriptome prediction and annotation in Ficus carica L.

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