Genera Of Rosaceae Research Articles

The complete chloroplast genome of Photinia davidsoniae: molecular structures and comparative analysis

Photinia davidsoniae is a common ornamental arbor in the genus Photinia (family Rosaceae). Here, we sequenced and assembled the complete plastome of P. davidsoniae using the next-generation DNA sequencing technology. And we then compared it with nine Photinia species using a range of bioinformatics software tools. The ten plastomes had sizes ranging from 159,230 bp for P. beckii to 160,346 bp for P. davidsoniae. They all had a conservative quartile structure. It contained two single-copy regions: a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeat (IR) regions. Each of the plastomes encoded 113 unique genes, including 79 protein-coding genes, four rRNA genes, and 30 tRNA genes. Furthermore, we detected six hypervariable regions (matK-rps16, rpoB-trnC, trnT-psbD, ndhC-trnV, psbE-petL, ndhF-rpl32-trnL), which could be used as potential molecular markers. We constructed two phylogenetic trees with plastomes or concatenated protein sequences of 25 species of 8 genera of Rosaceae. The tree constructed with complete plastomes has much stronger support. The results placed P. davidsoniae in the upper part of the phylogenetic tree. It shows that P. davidsoniae and P. lanuginosa are closely related. In summary, the plastomes of Photinia are conserved overall but carry significant minor variations, as expected. The results will be indispensable for distinguishing species, understanding the interspecific diversity, and elucidating the evolutionary processes of Photinia species.

High Diversity of Cytospora Associated With Canker and Dieback of Rosaceae in China, With 10 New Species Described.

Cytospora canker is a destructive disease of numerous hosts and causes serious economic losses with a worldwide distribution. Identification of Cytospora species is difficult due to insufficient phylogenetic understanding and overlapped morphological characteristics. In this study, we provide an assessment of 23 Cytospora spp., which covered nine genera of Rosaceae, and focus on 13 species associated with symptomatic branch or twig canker and dieback disease in China. Through morphological observation and multilocus phylogeny of internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (LSU), actin (act), RNA polymerase II subunit (rpb2), translation elongation factor 1-α (tef1-α), and beta-tubulin (tub2) gene regions, the results indicate 13 distinct lineages with high branch support. These include 10 new Cytospora species, i.e., C. cinnamomea, C. cotoneastricola, C. mali-spectabilis, C. ochracea, C. olivacea, C. pruni-mume, C. rosicola, C. sorbina, C. tibetensis, and C. xinjiangensis and three known taxa including Cytospora erumpens, C. leucostoma, and C. parasitica. This study provides an initial understanding of the taxonomy of Cytospora associated with canker and dieback disease of Rosaceae in China.

Pollen morphology in Rubus (Rosaceae) and its taxonomic implications

Rubus is one of the most species-rich and most taxonomically challenging genera in Rosaceae. Pollen morphology of Rubus species has been described by many researchers but never in a comprehensive study. In this study, pollen morphology of 155 species and 13 varieties representing all 12 subgenera of Rubus was examined using scanning electron microscope to investigate whether pollen characters can help elucidate the challenging taxonomy in this genus. The results showed that the pollen grains of studied Rubus species are tricolporate, and pollen shape varies from suboblate, spheroidal, subprolate and prolate to perprolate. Exine ornamentation of examined pollen grains can be divided into six types and three subtypes. The pollen cluster analysis tree, which was performed using nine pollen characters, does not agree well with the traditional macromorphological classification and molecular phylogenetic trees based on DNA fragments. Except for subg. Chamaemorus and subg. Comaropsis, pollen morphology seems difficult to distinguish at subgeneric or sectional level, and consequently it lacks significant taxonomic value at these levels. Pollen morphology may not be considered a diagnostic feature for the division of subgenera and sections in Rubus. Though pollen morphology alone is not sufficient to elucidate or reconstruct the taxonomic relationships within Rubus, it can provide some useful information for the taxonomic treatment at specific level.

Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers.

Rubus ellipticus is a wild crop having less number of EST-SSR markers. First attempt was made towards the transcriptomics data analysis and generation of EST-SSR markers which were used in genetic diversity and transferability studies. Rubus ellipticus is a raspberry with yellow fruits, native to tropical and subtropical India and Asia. Leaves of Rubus ellipticus 'Kumarhatti' collection were utilized for cDNA library construction. More than 15 million sequencing reads were generated using NextSeq500 Illumina RNA-seq technology. The DNASTAR software was used for de novo assembly from which 7777 unigenes with an average length of 500bp was obtained. These unigenes were annotated using public databases, including NCBI non-redundant and gene ontology. De novo assembly of R. ellipticus unigenes found the highest similarity to apple than to other members of Rosaceae. This is the first attempt to use the Illumina platform of RNA sequencing and de novo assembly for R. ellipticus without a reference genome. In this study, unigenes were used for SSR marker development. ESTs containing SSR motifs were extracted using an online Microsatellite Identification Tool (MISA). SSR primers were designed from the SSR containing 704 EST sequences using the Websat software. Total 304 EST-SSRs primers were successfully designed, out of which 68 randomly selected primer pairs were custom synthesized and used for validation. Real-time PCR was also performed to analyze the relationship of transcriptional factors with fruit ripening. Out of 68 primer pairs, 61 were found to be informative in R. ellipticus, whereas 65 primer pairs were informative in the five tested genera of Rosaceae, i.e., pear, peach, apple, rose, and strawberry with 95.3% and 93.5% polymorphism, leading to the conclusion that these marker systems are very efficient to carryout diversity and cross transferability study in Rosaceae genera.

Lectotypification of fifteen names of Rubus L. (Rosaceae) mainly from the Hengduan Mountains, China

Rubus Linnaeus (1753: 492), one of the most taxonomically challenging genera in Rosaceae (Lu 1983, Alice & Campbell 1999, Alice et al. 2008), comprises more than 700 species (Lu & Boufford 2003) and is distributed across the world except Antarctica (Alice & Campbell 1999). The Hengduan Mountains, the mountains at the eastern end of the Himalayas, are widely regarded as a global biodiversity hotspot. During a taxonomic revision of Rubus L. in the Hengduan Mountains and its neighbouring regions, we found that fifteen names have never been typified. Lectotypification of these names are designated here after examination of previous works (Zandee & Kalkman 1981, Kalkman 1984 & 1987, Monasterio-Huelin & Castroviejol 1993, Monasterio-Huelin 1996, Monasterio-Huelin & Webert 1996, Bean 1997a & b, Allen 1998, Widrlechner 1998, Matzke-Hajek 2001a & b, Sennikov & Weber 2010, Deng 2015, Weber 2015a & b, Gupta et al. 2016, Yang et al. 2016, Beek et al. 2017, Dash & Gupta 2017, Király 2017, Király et al. 2017).

Characterization of EST-SSR Among Six Genera of Rosaceae

EST-SSR is a molecular marker based on functional genomics,had been widely used because of its evenly distributed among the genome,better universality between species or genera and characters associated with the phenotypic traits.We downloaded the EST sequences of six genera in Rosaceae(Rosa,Malus,Pyrus,Prunus,Fragaria and Rubus) to study the distributed characteristic of SSR in Rosaceae by bioinformatics methods.There was significant difference of EST-SSR distribution frequency among genera,from 10.94%(Rubus) to 43.49%(Pyrus).The dinucleotide and trinucleotide repeats were the major types,AG/CT,GA/TC and AT/TA were the preponderant dinucleotide motifs,the trinucleotide repeats showed significant difference among genera,and the dominant type included AGA/TCT,GAA/TTC,AAG/CTT,CAC/GTG and ACA/TGT.Our results provided a research platform for plant molecular phylogeny and evolution,germplasm identification,genetic diversity and genetic mapping of Rosaceae.

Rosaceae conserved orthologous set (RosCOS) markers as a tool to assess genome synteny between Malus and Fragaria

Intertribal comparisons of genome synteny between phylogenetically distant genera in Rosaceae, such as Malus (apple) and Fragaria (strawberry), have previously been hampered by a lack of transferable markers that can be used as anchor points between genetic maps. The availability of conserved orthologous set (COS) markers recently developed for this family, coupled with the release of the Malus × domestica and Fragaria vesca draft genome sequences, provide new tools for comprehensive pairwise comparisons. The genetic mapping of 56 Rosaceae COS (RosCOS) markers revealed 21 regions of genomic synteny between apple and strawberry. Information concerning the location of RosCOS markers on 15 of 17 apple linkage groups (LG) and all seven LG of strawberry was used to assess the ancestral relationships between the two genera. Four differences in orientation of ancestral chromosome fragments on extant LG were identified in comparison with previous studies, as well as two potential insertions, two potential translocations, and two potential inversions. The set of orthologous markers developed for use in genetic mapping in Rosaceae, in combination with high-throughput analysis, will allow the exploration of chromosome evolution and refinement of ancestral relationships within the family, orientation, and anchoring of genome sequences as they become available and provide resources to develop markers for nonsequenced genomes within the family.

PrunusandOemleria(Rosaceae) Flowers from the Late Early Eocene Republic Flora of Northeastern Washington State, U.S.A.

Two genera of Rosaceae are described from the latest early Eocene Republic flora of northeastern Washington State, United States. Prunus cathybrownae sp. nov. (Rosaceae: subfamily Spiraeoideae, tribe Amygdaleae sensu Potter et al.) is based on eight flowers, including one containing in situ pollen and two immature fruits. Flowers are actinomorphic, perigynous, and pentamerous, with a campanulate hypanthium bearing five sepals. The gynoecium is unicarpellate and consists of a distally flared, bilobed stigma; an elongate style; and an ellipsoid, bilaterally asymmetric ovary. Two whorls of stamens—an inner one in which stamens are reflexed and an outer whorl of extended stamens—are both inserted into the hypanthium. Pollen from the outer whorl is 20 μm in diameter and tricolporate with a striately ornamented exine; clusters of smaller, presumably immature grains 7 μm long and 4 μm wide lacking distinctive ornamentation were recovered from the inner whorl. Immature fruits differ from the flowers in either having a senescent style or lacking one entirely and having fewer remnants of perianth parts and a larger and more symmetrical ovary. A second flower, Oemleria janhartfordae sp. nov. (Rosaceae: subfamily Spiraeoideae, tribe Osmaronieae sensu Potter et al.) is actinomorphic and perigynous and has five free pistils that each resemble the solitary pistil of Prunus. These include a flattened, bilobed stigma and an ellipsoid, bilaterally asymmetric ovary. The fossil has the laterally fixed, elongate style characteristic of the genus. These fossils are the oldest known floral examples of these two genera and demonstrate that both Prunus and Oemleria were present in the latest early Eocene in western North America. The Okanogan Highlands floristic province provides the earliest fossil evidence to date for the first major radiation of the Rosaceae, an important mostly temperate, mostly Northern Hemisphere family.

Rose ( Rosa hybrida L.) EST-derived microsatellite markers and their transferability to strawberry ( Fragaria spp.)

The ‘Genome database for Rosaceae (GDR)’ provides a large collection of expressed sequence tags (ESTs) harboring simple sequence repeats (SSRs) from several Rosaceae genera, including Rosa (rose). Primer pairs flanking SSR were designed for 312 unique Rosa ESTs based on GDR database. Eight rose ( Rosa hybrida L.) genotypes were tested for PCR amplification, and 287 (92%) of the primer pairs generated allele-specific PCR bands that were readily scored. From 183 (63.7%) primer pairs that evidenced polymorphic alleles among the eight rose cultivars, 20 pairs evidencing EST sequence homology to known gene functions and high levels of polymorphism were selected and utilized for DNA fingerprinting and genetic diversity assessments of 47 rose hybrids. A total of 202 polymorphic bands were scored and generated unique fingerprints for each rose hybrid. The Nei–Li genetic similarity coefficients among 1081 pair-wise comparisons of 47 cultivars exhibited a broad range of genetic variations from 0.30 (‘Grand King’ and ‘Carnival’) to 0.99 (‘First Red’ and ‘Red Champ’). UPGMA cluster analysis divided 47 hybrids into five major groups and two sub-groups. The cross-species transferability of 273 EST-SSR primer pairs was evaluated using four genotypes of the strawberry, a genus member of the Rosaceae family. PCRs on the DNA samples of strawberry were successful for 165 primer pairs; among these, 123 pairs amplified 243 polymorphic bands. As surrogates of the marker transfer, the phenetic relationship among the four strawberry genotypes was evaluated. Genetic similarity coefficients varied from 0.78 (‘Maehyang’ and ‘Janghyee’) to 0.64 (‘Janghyee’ and ‘Pragana’). The results of cluster analysis showed that the three octaploid strawberry cultivars were quite similar, whereas the diploid ‘Pragana’ was related distantly at the genomic DNA level. The EST-SSR markers developed in the present study can be efficiently utilized for genetic diversity studies in Rosaceae.

Prunus microsatellite marker transferability across rosaceous crops

A total of 145 microsatellite primer pairs from Prunus DNA sequences were studied for transferability in a set of eight cultivars from nine rosaceous species (almond, peach, apricot, Japanese plum, European plum, cherry, apple, pear, and strawberry), 25 each of almond genomic, peach genomic, peach expressed sequence tags (EST), and Japanese plum genomic, 22 of almond EST, and 23 of apricot (13 EST and 10 genomic), all known to produce single-locus and polymorphic simple-sequence repeats in the species where they were developed. Most primer pairs (83.6%) amplified bands of the expected size range in other Prunus. Transferability, i.e., the proportion of microsatellites that amplified and were polymorphic, was also high in Prunus (63.9%). Almond and Japanese plum were the most variable among the diploid species (all but the hexaploid European plum) and peach the least polymorphic. Thirty-one microsatellites amplified and were polymorphic in all Prunus species studied, 12 of which, covering its whole genome, are proposed as the “universal Prunus set”. In contrast, only 16.3% were transferable in species of other Rosaceae genera (apple, pear, and strawberry). Polymorphic Prunus microsatellites also detected lower levels of variability in the non-congeneric species. No significant differences were detected in transferability and the ability to detect variability between microsatellites of EST and genomic origin.

Using DNA Barcodes to Identify Rosaceae

DNA barcoding has recently been proposed as a technique that employs a short, standardized gene region to identify species. DNA barcoding is well established in animals because of a widely appropriate sequence for them, the cytochrome coxidase 1 [1], but there is not any universally accepted barcode for plants till now. Therefore, the primary task for barcoding plants is to find more useful barcodes that can identify as many species as possible. Medicinal plants have been used as traditional Chinese drugs for treating diseases, some of them are similar in morphology, and are often misidentified by chemical fingerprints. Rosaceae includes many medicinal plants with similar morphology and are usually hard to be identified. Here, we chose five potential barcodes, Universal Plastid Amplicon (matK, rpoB, rpoC1, rbcL) and the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS), to identify species from different genera in Rosaceae. The results suggest that the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) is a candidate to discriminate all of plant species in Rosaceae. Acknowledgements: We thank all my teachers and classmates in our laboratory very much for their help.

Introduction to the 2005 IBC symposium papers on the evolution of Rosaceae

Evolution of the Rosaceae has been studied tives on this family, particularly on its phylog extensively because the family contains imporeny, reproductive biology, and fossil record, tant plants. Many species in the family, such as Potter et al. analyzed a large data set of apples (Malus) and strawberries {Fragaria), molecular sequences, including four chloro have commercially valuable edible fruits. plast and six nuclear regions. They sampled all Roses {Rosa), cherries {Prunus), and other but a few genera of Rosaceae, and those that members of the family are prized horticulturwere not sampled were judged, based on ally. Blackberries {Rubus), cinqfoils {Potenmorphological and other data, to belong to tilla), and other groups are significant one or more clades strongly supported by the members in North Temperate ecosystems. molecular data. Potter et al.'s data consistently Rosaceae have also attracted the attention of resolved many clades that correspond more or evolutionary and systematic biologists because less closely to previously recognized supragen of their reproductive biology. Hybridization is eric taxa. However, despite the large amount frequent between species, but also occurs of data, relationships among many of these between some genera of what has been comclades were not resolved. Potter et al. trans monly known as subfamily Maloideae until lated their phylogeny into a classification with now (see below) and, in fact, has been three subfamilies. Rosoideae is more narrowly implicated in the origin of this group as well. circumscribed than it traditionally is but con Hybridization is associated with extensive sistently with recent molecular, morphological, polyploidy and, like two other large and and ontogenetic studies. Dryadoideae corn important families, Asteraceae and Poaceae, prise just the four actinorhizal genera of with gametophytic apomixis. This combinaRosaceae, and Spiraeoideae encompass all tion of hybridization, polyploidy, and apogroups assigned to the previously recognized mixis has created complex taxonomies in Amygdaloideae and Maloideae, as well as Crataegus, Potentilla, Rubus, Rosa and other numerous other groups. This classification genera. The symposium on the evolution of represents over a decade of studies in Rosaceae Rosaceae at the 2005 International Botanical and a significant advance in our understanding Congress in Vienna assembled diverse perspecof evolutionary relationships in the family.

Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits

New microsatellites markers [simple sequence repeat (SSR)] have been isolated from rose and integrated into an existing amplified fragment-length polymorphism genetic map. This new map was used to identify quantitative trait locus (QTL) controlling date of flowering and number of petals. From a rose bud expressed sequence tag (EST) database of 2,556 unigenes and a rose genomic library, 44 EST-SSRs and 20 genomic-SSR markers were developed, respectively. These new rose SSRs were used to expand genetic maps of the rose interspecific F-1 progeny. In addition, SSRs from other Rosaceae genera were also tested in the mapping progeny. Genetic maps for the two parents of the progeny were constructed using pseudo-testcross mapping strategy. The maps consist of seven linkage groups of 105 markers covering 432 cM for the maternal map and 136 markers covering 438 cM for the paternal map. Homologous relationships among linkage groups between the maternal and paternal maps were established using SSR markers. Loci controlling flowering traits were localised on genetic maps as a major gene and QTL for the number of petals and a QTL for the blooming date. New SSR markers developed in this study will provide tools for the establishment of a consensus linkage map for roses that combine traits and markers in various rose genetic maps.

Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy

Prunus is a large and economically important genus with considerable morphological variation. The evolution of vegetative and reproductive characters are examined here by parsimony reconstruction on trees obtained from data of ITS, trnL-trnF, trnS-trnG, and 25 morphological characters of 37 species of Prunus and representatives of eight other genera of Rosaceae. Prunus grayana is supported as the sister species to the rest of Prunus and the common ancestor of Prunus is reconstructed as having deciduous and serrated leaves, leafy racemes and fruit with well-developed pericarp. All diagnostic characters used in classification of the raceme-bearing species show some degree of convergent evolution and do not reflect phylogenetic relatedness. Some character states, such as evergreen foliage and entire leaf margin, are likely adaptations to environments with higher humidity and mean temperature. However, these hypotheses need to be tested by including species formerly classified in genus Pygeum, which were not available for this study. A clade consisting of subgenera Prunus, Amygdalus, Emplectocladus and section Microcerasus (formerly in subgenus Cerasus) is characterized by having axillary buds organized in groups of three, two of which give rise to flowers or inflorescences and one to a vegetative shoot. Fruits with thin pericarps are common in Prunus but they arose more than once independently. Dry fruits also evolved more than once, and only in species of Prunus living in arid environments, suggesting that this feature is another example of adaptation. Maddenia hypoleuca is nested within Prunus and the morphological characters used to segregate it from Prunus have been misinterpreted or are also found in species of Prunus previously classified in genus Pygeum.

Strawberry GenBank-derived and Genomic Simple Sequence Repeat (SSR) Markers and Their Utility with Strawberry, Blackberry, and Red and Black Raspberry

Although simple sequence repeat (SSR) markers have been developed for species in the closely related genera Fragaria L. (strawberry) and Rubus L. (raspberry and blackberry), the number of SSRs available is insufficient for genetic mapping. Our objective was to use and compare multiple approaches for developing additional SSRs for Fragaria and Rubus. The approaches included: the development of SSRs from GenBank sequences from species of varied relatedness to Fragaria and Rubus and identified with two different data-mining methods (BLAST and SSRIT); the evaluation of some previously published SSRs designed from related species; and the development of SSRs from a genomic library made from F. ×ananassa Duschene ex Rozier `Earliglow'. When an SSR was developed from a known gene sequence, the location of the repeat in the gene was determined to evaluate the effect on amplification and polymorphism detection. Cross-generic amplification between closely related Fragaria and Rubus as well as transference from species of varied relatedness to Fragaria and Rubus also was evaluated and indicated limited transference within the subfamily Rosoideae. However, development of SSRs for Fragaria and Rubus from Rosa L. (rose) and Rosaceae genera outside Rosoideae was not efficient enough to be practical for new map development. SSRIT was superior to BLAST for identifying GenBank sequences containing repeats. SSRs developed from repeats found in either the 5′UTR (80% polymorphic) or 3′UTR (85% polymorphic) were most likely to detect polymorphisms, compared with those developed from coding regions (30%). SSRs developed from the genomic library were only slightly superior to GenBank-derived SSRs in their ability to detect polymorphisms.

Triglyceride Composition of Oil from Stones of Nine Rosaceae Plants

Oil from stones of nine plants representing seven Rosaceae genera was studied by reversed-phase HPLC with refractive-index detection. Internal normalization using the incremental approach determined the qualitative and quantitative composition of the oil triglycerides. Triglycerides of Cerasus vulgaris Mill., C. avium Moench., and Prunus padus consisted of palmitic, stearic, oleic, linoleic, and C18:3 (α-eleostearic) acids. Triglycerides of Prunus tomentosa Thunb. Wall., P. domestica L., Armeniaca vulgaris Lam., P. persica (L.) Batsch, nectarine, and P. amygdalinus did not contain C18:3 acid.

Comparative Anatomy of the Secondary Phloem of Ten Species of Rosaceae

The anatomy of the secondary phloem of species belonging to four genera in Rosaceae is described. The three genera of the Maloideae studied are more or less similar in their phloem anatomy; tangential bands of fibresclereids alternate with bands of sieve elements, companion cells and parenchyma cells; superficially, the nonconducting and conducting phloem are not distinct from one another; sieve plates are compound and there are conspicuous sieve areas on lateral walls; rays are uniseriate and multiseriate, and homocellular. In the five species of Prunus (Prunoideae) studied, there are no fibre-sclereids in the conducting phloem, end walls bearing simple sieve plates are oblique to nearly horizontal; and rays are uniseriate and multiseriate, homocellular.

The genera of Rosaceae in the southeastern United States [concl.

The genera of Rosaceae in the southeastern United States [concl.

The genera of Rosaceae in the southeastern United States [cont.

The genera of Rosaceae in the southeastern United States [cont.