Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family

Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.

Molecular phylogeny and inflorescence evolution of Prunus(Rosaceae)based on RAD-seq and genome skimming analyses

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups.Both nuclear and plastome data recovered a well-resolved phylogeny.The species were divided into three main clades corresponding to their inflorescence types,-the racemose group,the solitary-flower group and the corymbose group-with the latter two sister to one another.Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago.The diversification of the three major clades began between the Paleocene and Miocene,suggesting that paleoclimatic events were an important driving force for Prunus diversification.Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences,and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis,respectively.We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies.Prunus has undergone extensive hybridization events,although it is difficult to identify conclusively specific instances of hybridization when using SNP data,especially deep in the phylogeny.Our study provides well-resolved nuclear and plastid phylogenies of Prunus,reveals substantial cytonuclear discord at shallow scales,and sheds new light on inflorescence evolution in this economically important lineage.

Comparative genomic analysis of N6-methyladenosine regulators in nine rosaceae species and functional characterization in response to drought stress in pear

N 6-methylated adenine(m6 A)is an emerging epigenetic marker in eukaryotic organisms that plays an important role in biological functions and in enriching genetic information.m6 A exerts these functions via the dynamic interplay among m6 A writers,erasers,and readers.However,little is known about the underlying mechanisms of m6 A in plant growth and stress responses.Here,we identified 276 masked m6 A regulators from nine Rosaceae species(Pyrus bretschneideri,Pyrus betulifolia,Pyrus communis,Malus domestica,Fragaria vesca,Prunus avium,Prunus mume,Prunus persica,and Rubus occidentalis).We classified and named these genes in more detail based on phylogenetic and synteny analysis.The expansion of m6 A regulators in Maloideae was dated back to the recent whole-genome duplication(WGD)in Rosaceae.Based on the expression pattern analysis and gene structure analysis of m6 A regulators,m6 A was shown to be a significant factor in regulating plant development and resistance.In addition,PbrMTA1-silenced pear plants displayed significantly reduced drought tolerance and chlorophyll content,as well as increased electrolyte leakage and concentrations of malondialdehyde and H2 O2.

Genome-wide identification and characterization of the IPT family members in nine Rosaceae species and a functional analysis of MdIPT5b in cold resistance

Cytokinins are members of a group of phytohormones involved in various growth and developmental processes in plants.Isopentenyl transferase(IPT)is the rate-limiting enzyme in catalyzing the biosynthesis of cytokinins.In this study,to understand the role of IPT family in cold resistance,78 IPT candidates were identified and characterized in nine Rosaceae genomes.The expansion of IPT families in the Rosaceae primarily occurred through segmental duplication rather than tandem duplication.In general,purifying selection controlled the evolution of IPT families in the Rosaceae,with IPT3 and IPT5 homologs as the primary drivers of evolution.Cis-elements,which are involved in the responses to many environmental stresses or phytohormone signals,were identified in the promoters of MdIPT members.This was consistent with the trends of expression of the MdIPT genes in apple(Malus domestica)calli.MdIPT5b was also found to exhibit multiple responses to phytohormones and stress signals.The ectopic expression of MdIPT5b resulted in an increase in cold resistance in transformed apple calli and tomato(Solanum lycopersicum)plantlets.The redox balance was partially stabilized through the accumulation of proline under cold stress.However,the ascorbate–glutathione cycle cannot be stabilized in the cold.All physiological and biochemical assays are preformed in spectrophotometer.These results showed that regulating the expression of IPT genes for moderate cytokinin improvement could enhance the accumulation of proline to stabilize the osmotic and redox balances to improve resistance to cold stress.

Evolution of the R2R3-MYB gene family in six Rosaceae species and expression in woodland strawberry

R2R3-MYB gene family play important roles in plants development, metabolism, and responses to various biotic and abiotic stresses. In this study, 838 R2 R3-MYB genes were identified from six Rosaceae species, including 105 in woodland strawberry(Fragaria vesca), 173 in European pear(Pyrus communis), 219 in apple(Malus domestica), 121 in peach(Prunus persica), 121 in Chinese rose(Rosa chinensis), and 99 in black raspberry(Rubus occidentalis). All R2 R3-MYB genes in the six Rosaceae species were clustered into 51 species-specific duplicated clades with 109 genes and 50 lineage-specific duplicated clades with 242 genes according to phylogenetic analysis. R2 R3-MYB genes were distributed on all chromosomes in each of the six species, with a small amount of tandem duplication events. The proportion of tandem repeat genes ranged from 0 to 25.1%. The R2 R3-MYB protein was conserved in a clade and likely to share similar functions. The distribution of Ks showed the duplication times of R2 R3-MYB genes in six Rosaceae species. Furthermore, most of the R2 R3-MYB genes had Ka/Ks values less than 1, which indicated they were driven by purifying selection during the evolutionary processes. The GO term enrichment analysis revealed that R2 R3-MYB genes in strawberry and black raspberry were more divergent than in other Rosaceae species. Analysis of transcriptomes of 42 different tissues and development stages of woodland strawberry showed that high expression levels of R2 R3-MYB suggested that the R2 R3-MYB genes in strawberry played a key role in growth and development of both vegetative tissues and fruits. The strawberry R2 R3-MYB genes in sub-group of S1, S2, S11, S20, and S22 had high expression levels both in young leaves(YL) and old leaves(OL) strawberry tissues under drought treatments.

Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

Mutants lacking wild-type MLO(Mildew resistance Locus O)proteins show broad-spectrum resistance to the powdery mildew fungus,and dysregulated cell death control,with spontaneous cell death in response to developmental or abiotic stimuli.In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants,we analysed systematically genome-wide data from Fragaria vesca,Prunus persica,Prunus mume,Malus domestica,Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods.Using three phylogenetic methods(the neighbour-joining,maximum likelihood,and Bayesian methods),we identified 117 MLO genes from 6 Rosaceae species.The results of all three phylogenetic analysis methods supported that these genes were divided into six clades.Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues.The findings indicated that motif 2 might be shared by the MLO gene family.The structural features of these genes showed large variations in sequence length among different species,although the lengths and the numbers of exons exhibited high degrees of similarity.Selective pressure analysis showed extremely significant differences in all 6 clades,with 2,1,and 1 site(s)under significant positive selection detected in clades III,IV,and VI,respectively.These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes.Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes.Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process.However,clade I may have undergone extensive altered functional constraints as a specialised functional role.Moreover,the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew,which then gradually evolved into functions such as the regulation of flower development,the control of root morphology,and seed evolution due to the different evolutionary rates after gene duplication.These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.

The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

The Rosaceae family has striking phenotypic diversity and high syntenic conservation.Gillenia trifoliata is sister species to the Maleae tribe of apple and~1000 other species.Gillenia has many putative ancestral features,such as herb/sub-shrub habit,dry fruit-bearing and nine base chromosomes.This coalescence of ancestral characters in a phylogenetically important species,positions Gillenia as a‘rosetta stone'for translational science within Rosaceae.We present genomic and phenological resources to facilitate the use of Gillenia for this purpose.The Gillenia genome is the fi rst fully annotated chromosome-level assembly with an ancestral genome complement(x=9),and with it we developed an improved model of the Rosaceae ancestral genome.MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fl eshy fruit development in Rosaceae.

Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae

This paper is the seventh in the Fungal Diversity Notes series,where 131 taxa accommodated in 28 families are mainly described from Rosa(Rosaceae)and a few other hosts.Novel fungal taxa are described in the present study,including 17 new genera,93 new species,four combinations,a sexual record for a species and new host records for 16 species.Bhatiellae,Cycasicola,Dactylidina,Embarria,Hawksworthiana,Italica,Melanocucurbitaria,Melanodiplodia,Monoseptella,Uzbekistanica,Neoconiothyrium,Neopaucispora,Pararoussoella,Paraxylaria,Marjia,Sporormurispora and Xenomassariosphaeria are introduced as new ascomycete genera.We also introduce the new species Absidia jindoensis,Alternaria doliconidium,A.hampshirensis,Angustimassarina rosarum,Astragalicola vasilyevae,Backusella locustae,Bartalinia rosicola,Bhatiellae rosae,Broomella rosae,Castanediella camelliae,Coelodictyosporium rosarum,Comoclathris rosae,C.rosarum,Comoclathris rosigena,Coniochaeta baysunika,C.rosae,Cycasicola goaensis,Dactylidina shoemakeri,Dematiopleospora donetzica,D.rosicola,D.salsolae,Diaporthe rosae,D.rosicola,Endoconidioma rosaehissaricae,Epicoccum rosae,Hawksworthiana clematidicola,H.lonicerae,Italica achilleae,Keissleriella phragmiticola,K.rosacearum,K.rosae,K.rosarum,Lophiostoma rosae,Marjia tianschanica,M.uzbekistanica,Melanocucurbitaria uzbekistanica,Melanodiplodia tianschanica,Monoseptella rosae,Mucor fluvius,Muriformistrickeria rosae,Murilentithecium rosae,Neoascochyta rosicola,Neoconiothyrium rosae,Neopaucispora rosaecae,Neosetophoma rosarum,N.rosae,N.rosigena,Neostagonospora artemisiae,Ophiobolus artemisiicola,Paraconiothyrium rosae,Paraphaeosphaeria rosae,P.rosicola,Pararoussoella rosarum,Parathyridaria rosae,Paraxylaria rosacearum,Penicillium acidum,P.aquaticum,Phragmocamarosporium rosae,Pleospora rosae,P.rosae-caninae,Poaceicola agrostina,P.arundinicola,P.rosae,Populocrescentia ammophilae,P.rosae,Pseudocamarosporium pteleae,P.ulmi-minoris,Pseudocercospora rosae,Pseudopithomyces rosae,Pseudostrickeria rosae,Sclerostagonospora lathyri,S.rosae,S.rosicola,Seimatosporium rosigenum,S.rosicola,Seiridium rosarum,Setoseptoria arundelensis,S.englandensis,S.lulworthcovensis,Sigarispora agrostidis,S.caryophyllacearum,S.junci,S.medicaginicola,S.rosicola,S.scrophulariae,S.thymi,Sporormurispora atraphaxidis,S.pruni,Suttonomyces rosae,Umbelopsis sinsidoensis,Uzbekistanica rosaehissaricae,U.yakutkhanika,Wojnowicia rosicola,Xenomassariosphaeria rosae.New host records are provided for Amandinea punctata,Angustimassarina quercicola,Diaporthe rhusicola,D.eres,D.foeniculina,D.rudis,Diplodia seriata,Dothiorella iberica,Lasiodiplodia theobromae,Lecidella elaeochroma,Muriformistrickeria rubi,Neofusicoccum australe,Paraphaeosphaeria michotii,Pleurophoma pleurospora,Sigarispora caulium and Teichospora rubriostiolata.The new combinations are Dactylidina dactylidis(=Allophaeosphaeria dactylidis),Embarria clematidis(=Allophaeosphaeria clematidis),Hawksworthiana alliariae(=Dematiopleospora alliariae)and Italica luzulae(=Dematiopleospora luzulae).This study also provides some insights into the diversity of fungi on Rosa species and especially those on Rosa spines that resulted in the characterisation of eight new genera,45 new species,and nine new host records.We also collected taxa from Rosa stems and there was 31%(20/65)overlap with taxa found on stems with that on spines.Because of the limited and non-targeted sampling for comparison with collections from spines and stems of the same host and location,it is not possible to say that the fungi on spines of Rosa differ from those on stems.The study however,does illustrate how spines are interesting substrates with high fungal biodiversity.This may be because of their hard structure resulting in slow decay and hence are suitable substrates leading to fungal colonisation.All data presented herein are based on morphological examination of specimens,coupled with phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Ocular rosacea without facial erythema involvement manifesting as bilateral multiple recurrent chalazions:A case report

BACKGROUND In addition to the non-specific symptomatology of ocular rosacea,currently,there are no reliable diagnostic tests for the disease,which may lead to its misdiagnosis.Here,we report a case of ocular rosacea presenting with multiple recurrent chalazion on both eyelids.CASE SUMMARY A 63-year-old female patient presented with multiple chalazion and dry eyes in both eyes,with no facial erythema.Initial management done were application of steroid eye ointment on both eyelids,hot compresses,and eyelid margin cleaning;noting that there was no relief of symptoms.Surgical excision of the chalazion was done on both eyes,however,bilateral recurrence occurred post-operatively.The pathological studies showed infiltration of a small amount of fibrous tissue with many chronic inflammatory cells.Immunohistochemistry studies were positive for LL-37.Resolution of the chalazion occurred after oral administration of doxycycline and azithromycin.CONCLUSION Our findings show that ophthalmologists should recognize the ocular manifestations of skin diseases.

中国枇杷属种质资源、品种和栽培管理(1)

枇杷是中国南方特产水果,春末夏初成熟,福建俗谚云：“四月枇杷满树金”,4月恰好是水果淡季,果肉柔软多汁,甜或甜酸适度,风味鲜美,富含人体需要的多种营养成分,是深受人们喜爱的伏季佳果名品。枇杷原产中国,属蔷薇科（Rosaceae）枇杷属（Eriobotrya）常绿乔木。中国四川汉源、泸定、会理、普格,湖北长阳、恩施等地尚有野生枇杷分布。

优质高产树莓生产园周年管理技术

树莓（raspberry）是蔷薇科（Rosaceae）悬钩子属（Rubus）多年生灌木类落叶果树,又名悬钩子、木莓、马林果等。果实色泽诱人、柔嫩多汁、风味独特,被誉为＂黄金水果＂和＂水果之王＂,果实富含花青素、SOD、黄酮、鞣化酸等抗氧化物质,具有多种保健功能,颇受国内外消费者青睐。辽宁省是树莓的适栽区,近年来树莓产业的发展突飞猛进,

樱花组织培养研究进展

樱花(P.serrulata)别名:山樱花、福岛樱、青山樱,泛指蔷薇科(Rosaceae),李亚科(Prunoidea),樱属(Cerasus)观赏植物,共120余种,有340个品种及改良的杂交品种。

辽西北地区树莓栽培的几项改进技术

树莓属蔷薇科（Rosaceae）悬钩子属（Rubus）多年生小灌木型落叶果树,是联合国粮农组织向世界推荐的＂第三代水果＂,果实富含鞣化酸、黄酮、SOD等保健成分,具有提高人体免疫力、抗氧化防衰老等作用。树莓除可鲜食外,还可以加工成果酒、饮料、浓缩汁、果酱、罐头等,还被广泛用于制药、保健品、化妆品等生产领域。

A New Compound from Chaenomeles sinensis (Thouin) Koehne

A new dihydrochromone derivative, named chaenomone, was isolated from the twigs of Chaenomeles sinensis (Thouin) Koehne. The structure was determined by spectroscopic methods.

Two New C-glucoside Flavonoids from Leaves of Crataegus pinnatifida Bge.var.major N.E.Br.

Two new C-glucoside flavonoids, namely 8-C-b-D-(2-O-acetyl) glucofuranosyl apigenin and 3-O-acetylvitexin, were isolated from leaves of Crataegus pinnatifida Bge. var. major N. E. Br.. Their structures were elucidated by the spectroscopic means and chemical evidence.

New Diterpenoid Alkaloids from Spiraea japonica var. Ovalifolia

Five new diterpenoid alkaloids. 19-O-deethlyspiramine N (1), deacetylspiramine S (2), spiramidine A (3), spiramidine B (4) and deacetylspiramine F (5) were isolated from the aerial parts of Spirae japonica L. f. var ovalifolia. Their structures were charaterized mainly based on spectral analysis.

A New Flavonoid Ketohexofuranoside from Leaves of Crataegus pinnatifida Bge.var. major N.E.Br.

A new flavonoid, namely pinnatifine I (1), was isolated from the leaves of Crataegus pinnatifida Bge. var. major N.E.Br.. Its structure was elucidated by spectroscopic analysis and chemical evidence.

A New Diterpene from Spiraea japonica var. ovalifolia

A new diterpenoid, 15-O-acetylspiraminol (1), was isolated from the aerial parts of Spireae japonica L. f. var. ovalifolia. The structure was charaterized mainly based on spectral analysis.

Two New Glycosides from Rubus amabilis

A pregnane glycoside and a lignan glycoside were isolated from the aerial parts of Rubus amabilis. Their structures were elucidated as 3-O-beta-D-glucopyranosyl-3 beta.15 alpha-dihydroxypregn-5-en-20-one and (-)-secoisolariciresinol-O-alpha-L-rhamnopyranoside using spectroscopic and chemical methods.

Two new triterpenes from Duchesnea indica

Two new triterpenes, 2α,3β-dihydroxyurs- 12-en- 18,19-epoxy-28-oic acid （1） and 18,19-seco, 2α, 2α-dihydroxyl-19-oxo-urs- 11,13（18）-dien-28-oic acid （2） were isolated from the herbaceous part of Duchesnea indica. Their structures were elucidated by spectroscopic analysis, including 2D NMR technique. The isolated compounds exhibited moderate cytotoxic activities against HeLa and L929 cell lines.