DNA N
6
-methyladenine (6 mA) is one of the most vital epigenetic modifications and involved in controlling the various gene expression levels. With the avalanche of DNA sequences generated in ...numerous databases, the accurate identification of 6 mA plays an essential role for understanding molecular mechanisms. Because the experimental approaches are time-consuming and costly, it is desirable to develop a computation model for rapidly and accurately identifying 6 mA. To the best of our knowledge, we first proposed a computational model named i6mA-Fuse to predict 6 mA sites from the Rosaceae genomes, especially in
Rosa chinensis
and
Fragaria vesca
. We implemented the five encoding schemes, i.e., mononucleotide binary, dinucleotide binary, k-space spectral nucleotide, k-mer, and electron–ion interaction pseudo potential compositions, to build the five, single-encoding random forest (RF) models. The i6mA-Fuse uses a linear regression model to combine the predicted probability scores of the five, single encoding-based RF models. The resultant species-specific i6mA-Fuse achieved remarkably high performances with AUCs of 0.982 and 0.978 and with MCCs of 0.869 and 0.858 on the independent datasets of
Rosa chinensis
and
Fragaria vesca
, respectively. In the
F. vesca
-specific i6mA-Fuse, the MBE and EIIP contributed to 75% and 25% of the total prediction; in the
R. chinensis
-specific i6mA-Fuse, Kmer, MBE, and EIIP contribute to 15%, 65%, and 20% of the total prediction. To assist high-throughput prediction for DNA 6 mA identification, the i6mA-Fuse is publicly accessible at
https://kurata14.bio.kyutech.ac.jp/i6mA-Fuse/
.
Key message
The existing prediction models are not suitable to identify 6mA in the Rosaceae genome because the existing algorithms are species-specific. Thus, a novel predictor is desired to be established to identify 6mA sites in the Rosaceae genome. To the best of our knowledge, we first propose a computation model named i6mA-Fuse (Identification of N6-MethylAdenine sites by Fusing multiple feature representation) to predict 6mA sites from the Rosaceae genomes, especially in
Rosa chinensis
and
Fragaria vesca
.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Abstract
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding ...data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.
Berries, especially members of several families, such as Rosaceae (strawberry, raspberry, blackberry), and Ericaceae (blueberry, cranberry), belong to the best dietary sources of bioactive compounds ...(BAC). They have delicious taste and flavor, have economic importance, and because of the antioxidant properties of BAC, they are of great interest also for nutritionists and food technologists due to the opportunity to use BAC as functional foods ingredients. The bioactive compounds in berries contain mainly phenolic compounds (phenolic acids, flavonoids, such as anthocyanins and flavonols, and tannins) and ascorbic acid. These compounds, either individually or combined, are responsible for various health benefits of berries, such as prevention of inflammation disorders, cardiovascular diseases, or protective effects to lower the risk of various cancers. In this review bioactive compounds of commonly consumed berries are described, as well as the factors influencing their antioxidant capacity and their health benefits.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been ...clarified.
With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family.
Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments.
Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many ...morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.
Potassium (K⁺) is the most abundant cation in plant cells necessary for plant growth and development. The uptake and transport of K⁺ are mainly completed through transporters and channels, and the ...Shaker family genes are the most studied K⁺ channels in plants. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified Shaker K⁺ channel gene family members in Rosaceae. We cloned and characterized a Shaker K⁺ channel KAT1 from pear (Pyrus × bretschneideri). In total, 36 Shaker K⁺ channel genes were identified from Rosaceae species and were classified into five subgroups based on structural characteristics and a phylogenetic analysis. Whole-genome and dispersed duplications were the primary forces underlying Shaker K⁺ channel gene family expansion in Rosaceae, and purifying selection played a key role in the evolution of Shaker K⁺ channel genes. β-Glucuronidase and qRT-PCR assays revealed that PbrKAT1 was mainly expressed in leaves, especially in guard cells. PbrKAT1 displayed a typical inward-rectifying current when expressed in Xenopus laevis oocytes. The activity of PbrKAT1 was inhibited by external sodium ions, possibly playing an important role in the regulation of salt tolerance in pear. These results provide valuable information on evolution, expression and functions of the Shaker K⁺ channel gene family in plants.
Even with recent reductions in sequencing costs, most plants lack the genomic resources required for successful short-read transcriptome analyses as performed routinely in model species. Several ...approaches for the analysis of short-read transcriptome data are reviewed for nonmodel species for which the genome of a close relative is used as the reference genome. Two approaches using a data set from Phytophthora-chaWenged Rubus idaeus (red raspberry) are compared. Over 70000000 86-nt Illumina reads derived from R. idaeus roots were aligned to the Fragaria vesca genome using publicly available informatics tools (Bowtie/TopHat and Cufflinks). Alignment identified 16956 putatively expressed genes. De novo assembly was performed with the same data set and a publicly available transcriptome assembler (Trinity). A BLAST search with a maximum e-value threshold of 1.0x10⁻³ revealed that over 36000 transcripts had matches to plants and over 500 to Phytophthora. Gene expression estimates from alignment to F vesca and de novo assembly were compared for raspberry (Pearson's correlation=0.730). Together, alignment to the genome of a close relative and de novo assembly constitute a powerful method of transcriptome analysis in nonmodel organisms. Alignment to the genome of a close relative provides a framework for differential expression testing if alignments are made to the predefined gene-space of a close relative and de novo assembly provides a more robust method of identifying unique sequences and sequences from other organisms in a system. These methods are considered experimental in nonmodel systems, but can be used to generate resources and specific testable hypotheses.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Summary
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.
Significance Statement
We used peach as a model to gain insight into the molecular basis of double flowers, an important trait in many ornamental plants. We propose that a deletion causes a TOE‐type transcription factor to escape miR172‐mediated repression, in turn resulting in an increased number of petals, as corroborated by results on the orthologous gene in rose.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
This paper presents the first quantitative ethnobotanical study of the flora in Toli Peer National Park of Azad Jammu and Kashmir, Pakistan. Being a remote area, there is a strong dependence by local ...people on ethnobotanical practices. Thus, we attempted to record the folk uses of the native plants of the area with a view to acknowledging and documenting the ethnobotanical knowledge. The aims of the study were to compile an inventory of the medicinal plants in the study area and to record the methods by which herbal drugs were prepared and administered.
Information on the therapeutic properties of medicinal plants was collected from 64 local inhabitants and herbalists using open ended and semi-structured questionnaires over the period Aug 2013-Jul 2014. The data were recorded into a synoptic table comprising an ethnobotanical inventory of plants, the parts used, therapeutic indications and modes of application or administration. Different ethnobotanical indices i.e. relative frequencies of citation (RFC), relative importance (RI), use value (UV) and informant consensus factor (Fic), were calculated for each of the recorded medicinal plants. In addition, a correlation analysis was performed using SPSS ver. 16 to check the level of association between use value and relative frequency of citation.
A total of 121 species of medicinal plants belonging to 57 families and 98 genera were recorded. The study area was dominated by herbaceous species (48%) with leaves (41%) as the most exploited plant part. The Lamiaceae and Rosaceae (9% each) were the dominant families in the study area. Among different methods of preparation, the most frequently used method was decoction (26 species) of different plant parts followed by use as juice and powder (24 species each), paste (22 species), chewing (16 species), extract (11 species), infusion (10 species) and poultice (8 species). The maximum Informant consensus factor (Fic) value was for gastro-intestinal, parasitic and hepatobiliary complaints (0.90). Berberis lycium Ajuga bracteosa, Prunella vulgaris, Adiantum capillus-veneris, Desmodium polycarpum, Pinus roxburgii, Albizia lebbeck, Cedrella serrata, Rosa brunonii, Punica granatum, Jasminum mesnyi and Zanthoxylum armatum were the most valuable plants with the highest UV, RFC and relative importance values. The Pearson correlation coefficient between UV and RFC (0.881) reflects a significant positive correlation between the use value and relative frequency of citation. The coefficient of determination indicated that 77% of the variability in UV could be explained in terms of RFC.
Systematic documentation of the medicinal plants in the Toli Peer National Park shows that the area is rich in plants with ethnomedicinal value and that the inhabitants of the area have significant knowledge about the use of such plants with herbal drugs commonly used to cure infirmities. The results of this study indicate that carrying out subsequent pharmacological and phytochemical investigations in this part of Pakistan could lead to new drug discoveries.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Rosaceae is an economically important plant family that can be affected by a multitude of pathogenic microbes, some of which can cause dramatic losses in production. As a type of pattern-recognition ...receptor, receptor-like proteins (RLPs) are considered vital regulators of plant immunity. Based on genome-wide identification, bioinformatic analysis, and functional determination, we investigated the evolutionary characteristics of RLPs, and specifically those that regulate Valsa canker, a devastating fungal disease affecting apple and pear production. A total of 3028 RLPs from the genomes of 19 species, including nine Rosaceae, were divided into 24 subfamilies. Five subfamilies and seven co-expression modules were found to be involved in the responses to Valsa canker signals of the resistant pear rootstock Pyrus betulifolia 'Duli-G03'. Fourteen RLPs were subsequently screened as candidate genes for regulation of resistance. Among these, PbeRP23 (Chr13.g24394) and PbeRP27 (Chr16.g31400) were identified as key resistance genes that rapidly enhance the resistance of 'Duli-G03' and strongly initiate immune responses, and hence they have potential for further functional exploration and breeding applications for resistance to Valsa canker. In addition, as a consequence of this work we have established optimal methods for the classification and screening of disease-resistant RLPs.
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