The Rosa genome provides new insights into the domestication of modern roses

Raymond, Olivier; Gouzy, Jérôme; Just, Jérémy; Badouin, Hélène; Verdenaud, Marion; Lemainque, Arnaud; Vergne, Philippe; Moja, Sandrine; Choisne, Nathalie; Pont, Caroline; Carrère, Sébastien; Caissard, Jean‐Claude; Couloux, Arnaud; Cottret, Ludovic; Aury, Jean‐Marc; Szécsi, Judit; Latrasse, David; Madoui, Mohammed‐Amin; François, Léa; Fu, Xiaopeng; Yang, Shuhua; Dubois, Annick; Piola, Florence; Larrieu, Antoine; Perez, Magali; Labadie, Karine; Perrier, Lauriane; Govetto, Benjamin; Labrousse, Yoan; Villand, Priscilla; Bardoux, Claudia; Boltz, Véronique; Roques, Céline; Heitzler, Pascal; Vernoux, Teva; Vandenbussche, Michiel; Quesneville, Hadi; Boualem, Adnane; Bendahmane, Abdelhafid; Liu, Chang; Bris, Manuel Le; Salse, Jérôme; Baudino, Sylvie; Benhamed, Moussa; Wincker, Patrick; Bendahmane, Mohammed

doi:10.1038/s41588-018-0110-3

Cited by 395 publications

(422 citation statements)

References 69 publications

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“…were "baited" out by ipyrad's mode "denovo-reference" using the complete mitochondiral genomes of Populus davidiana (KY216145.1) (Choi et al, 2017), Pyrus pyrifolia (KY563267.1) (Chung, Lee, Kim, & Kim, 2017) and Rosa chinensis (CM009589.1) (Raymond et al, 2018), and chloroplastidial genomes of Quercus rubra (JX970937.1) (Alexander & Woeste, 2014), Quercus aliena (KU240007.1) and…”

Section: Genomic Data Analysesmentioning

confidence: 99%

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Pina‐Martins

Baptista

Παππάς

et al. 2018

Global Change Biology

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Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species' evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, "Genotyping by sequencing" is used to derive 1,996 single nucleotide polymorphism markers to assess the species' evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species' genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species' gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. "Risk of Non-Adaptedness" (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms. K E Y W O R D Sassociation study, genotyping by sequencing, local adaptation, natural selection effects, Quercus suber, risk of non-adaptedness, West Mediterranean

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Section: Genomic Data Analysesmentioning

confidence: 99%

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Pina‐Martins

Baptista

Παππάς

et al. 2018

Global Change Biology

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“…We hypothesized that these two transcripts represent allelic variants of the rose ortholog of Prupe.6G242400 , and confirmed their existence by Sanger sequencing of genomic DNA and cDNA products from flower buds of the double‐flower rose ‘Meimarmoto’ (Figure a). This hypothesis was confirmed by mapping the RAG04721 transcript on the recently released rose genome assembly of the double‐flower Rosa chinensis ‘Old Blush’ (Raymond et al ., ): several retroelement‐like features were identified between the annotated gene model RchiOBHmChr3 g0468481 (chromosome 3: 14 492 546–14 495 427), which encodes the RAG04721 transcript (5′‐UTR plus exon I–exon VIII), and a region annotated as RchiOBHmChr3 g0468491 aligning to the 3′ portion of RAG04722 , located about 10 kb downstream of RchiOBHmChr3 g0468481 (chromosome 3: 14 505 776–14 506 765). This is consistent with an insertion within the TOE‐like gene encoding transcript RAG04722 .…”

Section: Resultsmentioning

confidence: 95%

“…Likewise, our data support the importance of a TOE‐type gene, rather than an AP2‐type gene, in determining flower doubleness in Rosaceae, as further supported by the identification of a mutation in the R. x hybrida ortholog to Prupe.6G242400 , which results in a transcript RAG04721 lacking the miR172 target site, similar to the peach ΔCter transcript. This variant originates from an insertion event also annotated in the recently released R. chinensis genome (Raymond et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Deletion of the miR172 target site in a TOE‐type gene is a strong candidate variant for dominant double‐flower trait in Rosaceae

et al. 2018

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Double flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants, including Prunus persica (peach), a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in five segregating progenies delimited Di2 to an interval spanning 150 858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic resequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait, and we showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co-segregated with the phenotype in 621 progenies, accounting for the dominant inheritance of the Di2 locus. Further corroborating the results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double-flower roses. Phylogenetic analysis showed that these two genes belong to a TARGET OF EAT (TOE)-type clade not represented in Arabidopsis, indicating a divergence of gene functions between AP2-type and TOE-type factors in Arabidopsis and other species. The identification of orthologous candidate genes for the double-flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.

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“…Among them, the positive sequences of Drosophila, Tolypocladium and yeast were downloaded from the MethSMRT [29] database (http://sysbio.sysu.edu.cn/methsmrt/), and the sequences described as "6mA"were deemed as the 6mA positive sequences. The positive sequences of Rice indica were derived from the eRice websites (http://www.elabcaas.cn/rice/downloads.html), while those of Arabidopsis thaliana [9] were collected from the NCBI Gene Expression Omnibus (GEO) with accession number GSE81596 (GSM2157793), and those of Fragaria vesca [30], and Rosa chinensis [31] were obtained from the MDR database (http://mdr.xieslab.org/).…”

Section: Including Arabidopsis Thaliana Fragaria Vesca Rosa Chinementioning

confidence: 99%

SICD6mA: Identifying 6mA Sites using Deep Memory Network

Liu

2020

Preprint

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Background:DNA N6-methyladenine (6mA) is a kind of epigenetic modification in prokaryotes and eukaryotes, which involves multiple biological processes, such as gene regulation and tumorigenesis. Identifying 6mA contributes to understand its regulatory role. Therefore, to satisfy the needs of large-scale preliminary screening, it is necessary to develop the high-quality computational models for the rapid identification of 6mA sites. However, the existing calculation approaches are mostly specific to rice, and they have not been extensively applied to human genome. Results:This study proposed a classification method of deep learning based on the memory mechanism namedSICD6mA. In addition, the large benchmark datasets were constructed for human and rice, respectively, which integrated the recently reported 6mA sites. According to the evaluation results, SICD6mA displayed favorable robustness during cross-validations, which achieved the area under the curve (AUC) values of 0.9824 and 0.9903 for Human and Rice's genomes in independent test evaluations, separately. Conclusions:The successful prediction rate of 6mA sites on cross-species genomes exhibited higher accuracy than that of the state-of-the-art methods. For the convenience of experimental scientists, the user-friendly tool SICD6mA was developed to predict the cross-species 6mA sites, thereby accelerating and facilitating future cross-species genome research. BackgroundDNA N6-methyladenine(6mA) refers to methylation at the N6site of adenine[1]. Typically, DNA 6mA modification is the most common DNA modification in prokaryotic genomes[2], which is once thought not to exist in eukaryotes[3] (including humans), because it is not detected in earlier studies. With the development of high-throughput sequencing technology, numerous 6mA modifications have been detected in different multicellular eukaryotes. In recent years, 6mA modification has been found to play an important role in DNA epigenetic modification of eukaryotes. DNA methylation represents a key element in epigenetic regulation, and DNA 6mA modification exerts a vital part in regulating gene expression[4], germ cell differentiation[5] etc. It has been reported in the genomes of E. coli[6], Drosophila melanogaster[7], rice[8], and Arabidopsis[9] etc.Currently, the 6mA sites can be detected in mouse and human cells using the sensitive detection technology. 6mA

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The Rosa genome provides new insights into the domestication of modern roses

Cited by 395 publications

References 69 publications

New insights into adaptation and population structure of cork oak using genotyping by sequencing

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Deletion of the miR172 target site in a TOE‐type gene is a strong candidate variant for dominant double‐flower trait in Rosaceae

SICD6mA: Identifying 6mA Sites using Deep Memory Network

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