A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes

Koyama, Takashi; Nakamoto, Masatoshi; Morishima, Kagayaki; Nagarkatti, Mitzi; Yamashita, Takefumi; Sasaki, Kohei; Kuruma, Yosuke; Mizuno, Naoki; Suzuki, Moe; okada, yoshiharu; Ieda, Risa; Uchino, Toshitaka; Tasumi, Satoshi; Hosoya, S.; Uno, Seiichi; Koyama, Jiro; Toyoda, Atsushi; Kikuchi, Kiyoshi; Sakamoto, Takashi

doi:10.1016/j.cub.2019.04.069

Cited by 93 publications

(97 citation statements)

References 82 publications

(94 reference statements)

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“…In general, it is thought that the sex of plants as well as animals is controlled by heteromorphic sex chromosomes, such as XY or ZW systems, or by sex-linked genome regions in which recombination is highly suppressed at the kb- or Mb-scale (Charlesworth, 2016). It was also recently reported that a single gene or a single base mutation in homomorphic chromosomes is involved in sex determination in amphibia and Seriola fish (Koyama et al, 2019; Miura, 2017). It therefore remains possible that sex determination could be controlled by a single gene in some plants, one of which may be fig.…”

Section: Discussionmentioning

confidence: 94%

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

Preprint

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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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Section: Discussionmentioning

confidence: 94%

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

Preprint

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“…Our simulations (Figure 8) provide insight into how to distinguish the mode of selection at a linked locus. Shortly after turnover, if divergence between male and female haplotypes is restricted in a very narrow region around the sex-determining locus, it may be likely that the sex-determining allele has become established with no help from linked selection (i.e., Myosho et al (2012); Kamiya et al (2012); Koyama et al (2019)). On the other hand, a highly diverged region spreads surrounding the sex-determining locus, the sex-determining allele has become established together with a linked allele at a sexually antagonistic locus, or sexually antagonistic loci arose after the establishment of the sex-determining locus.…”

Section: Discussionmentioning

confidence: 99%

Establishment of a new sex-determining allele driven by sexually antagonistic selection

Innan

Sakamoto

2020

Preprint

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Some species undergo frequent turnovers of sex-determining locus, rather than having stable diverged sex chromosomes. In such species, how often turnover occurs is a fundamental evolutionary question. We model the process with considering a linked locus under sexually antagonistic selection. The entire process of a turnover may be divided into two phases, which are referred to as the stochastic and deterministic phases. The stochastic phase is when a new sex-determining allele just arises and is still rare and random genetic drift plays an important role. In the deterministic phase, the new allele further increases in frequency by positive selection. The theoretical results currently available are for the deterministic phase, which demonstrated that a turnover of a newly arisen sex determining locus could benefit from selection at a linked locus under sexually antagonistic selection, by assuming that sexually antagonistic selection works in a form of balancing selection. In this work, we provide a comprehensive theoretical description of the entire process from the stochastic phase to the deterministic phase. In addition to balancing selection, we explore several other modes of selection on the linked locus. Our theory allows us make a quantitative argument on the rate of turnover and the effect of the mode of selection at the linked locus. We also performed simulations to explore the pattern of polymorphism around the new sex determining locus. We find that the pattern of polymorphism is informative to infer how selection worked through the turnover process.

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“…MD simulations have been applied to many phenomena of biological polymers (e.g. protein-protein interaction) [19][20][21][22][23][24] as well as chemical reactions [25][26][27]. In these studies, detection of structural change is essential.…”

Section: Multiplicity In Rbps In Living Cellsmentioning

confidence: 99%

Versatility of RNA-Binding Proteins in Living Cells

Kurokawa¹,

Takeuchi²,

Shiina³

et al. 2019

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This conference paper aims at demonstration of complexity or multiplicity of RNA-binding protein (RBP) and its related RNA. The data in the manuscript are based upon the third Annual Meeting of the RNA study group, held at the Tokyo office of the Kyoto University on May 23 in 2019. The purpose of the meeting is to present recent progress of the study group and have discussion regarding RNA and related molecules, especially focusing on RBP in this year. We had fourteen sessions and documented ten of them in the manuscript. There were exciting and fruitful debates. Actual presentations are shown as follows. Specific RBP Sfpq and Qk are involved in neuronal development in mouse system. Also in mouse, liquid-and solid-like RNA granule formation plays pivotal roles in neuronal functions. Biochemical experiments demonstrate that affinity profiles categorize RNA-Binding proteins into distinctive groups. This presents basis for biological divergence of RBPs. In the context of pathology, RNA aptamers against prion and Alzheimer's diseases may present therapeutic outcome. Computational analysis is another utility for approaching riddle of RBPs. The study of X-chromosome inactivation is pioneering field of long noncoding RNAs. Redundant triplex interactions between lncRNA and LINE-1s are supposed to be crucial in X-chromosome inactivation. Myogenesis-related lncRNA, Myoparr promotes skeletal muscle atrophy caused by denervation through the regulation of Riki Kurokawa et al.: Versatility of RNA-Binding Proteins in Living Cells GDF5/BMP14 expression. In neurodegenerative disorders functional loss of TLS/FUS induces onset of frontotemporal lobar degeneration. Conformational change of TLS is induced with binding of various nucleic acid molecules. TLS is also involved in phase separation into aggregation to pathogen generation of neurodegenerative diseases. The meeting has been successfully prorogued. We utilize the data to boost the activity of the field of RNA and RBP. The achievements of the meeting have confirmed pivotal roles of RBPs in living cells. It should be in complexity. We will be able to analyze intricate phenomena of RBP biological actions and contribute to uncover the veiled rules in divergent biological programs.

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A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes

Abstract: Highlights d A trans-species SNP in a steroidogenic Hsd17b1 determines sex in genus Seriola d The Z-linked allele of HSD17B1 attenuates E1 to E2 conversion activity d The data support a long-standing hypothesis on steroidinduced sex determination

Cited by 93 publications

References 82 publications

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

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

Establishment of a new sex-determining allele driven by sexually antagonistic selection

Versatility of RNA-Binding Proteins in Living Cells

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