Data_Sheet_1_Power Play of Commensal Bacteria in the Buccal Cavity of Female Nile Tilapia.docx

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.</p

MOESM1 of Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation

Additional file 1: Figure S1. Ranking of genotypes in the German ‘Idared’ × Malus ×robusta 5 population ordered by degree of infection 20–60 days after inoculation of floral clusters with Ea222_JKI. All data (2011 to 2013 and 2015 to 2017) available for a genotype were averaged for the mean score. Different colours indicate the percentages of the scores 0–6 for the floral clusters of a genotype

MOESM4 of Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation

Additional file 4: Table S1. Number of inoculated flower clusters per genotype, year and scoring results

MOESM3 of Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation

Additional file 3: Figure S3. Significant differences between mean resistance scores of genotypes in the German ‘Idared’ × Malus ×robusta 5 population. Only genotypes tested in all years of the respective period were utilized for the analysis. Genotypes without any symptoms in the respective period were removed from analyses, because of the lack of standard deviation. Different letters on the right side indicate significanet differences at a level of α = 0.05. a. Period 2011 to 2013. b. Period 2015 to 2017. c. Period 2011 to 201

MOESM2 of Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation

Additional file 2: Figure S2. Significant differences between mean resistance scores of individual years in the German ‘Idared’ × Malus ×robusta 5 population. Only genotypes tested in all years of the respective period were utilized for the analysis. The significance level is α = 0.05. a. Period 2011 to 2013. b. Period 2015 to 2017. c. Period 2011 to 201

Phylogenetic and gene expression analysis of the expansin-like genes from apple and European pear.

<p>A) Phylogenetic tree of predicted expansin-like genes from apple and European pear. Predicted expansin-like protein models from apple (MDP prefix) and European pear (PCP prefix) were aligned, and a conserved region of alignment of 313 residues was used to construct the phylogenetic tree Geneious 6.1.6 (Biomatters Ltd, Auckland, NZ). The linkage group (LG) of each model is shown where possible; some models are not anchored (LG-NA) to the genome. Models that represent the best hit for published expansins are labelled additionally as such. <i>DdEXP2</i> from <i>Dictyostelium discoideum</i> was used as an out-group. Bootstrap proportions for 100 trees were calculated and bootstrap values ≥50 are shown. Scale indicates 0.4 substitutions per site. EXPA, α-expansins; EXPB, β-expansins; EXLA, alpha-like expansins; EXLB, beta-like expansins <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092644#pone.0092644-Kende1" target="_blank">[50]</a>. mRNA-seq expression levels in ‘Comice’ melting pear (CM), ‘Nijisseki’ (NJ) crisp pear and ‘Royal Gala’ (RG) crisp apple, undergoing fruit ripening in storage show that one clade is strongly associated with fruit ripening (coloured green). The inserted graph shows the expression analysis by qPCR of <i>EXP2</i> in fruit at harvest and during storage, which corresponds to the mRNA-seq data. Yellow bars: RG, red bars CM, orange bars NJ). RPKM: Reads Per Kilobase per Million mapped reads. Single arrow shows the apple expansin (MdEXPA7) mapped to a quantitative trait locus for fruit texture. B) Alignment of the first 170 bp of apple and pear homologues, demonstrating genome duplication preceded speciation.</p

Classification of repeated elements in European pear based on the ‘Rosaceae’ clade from RepBase.

<p>Classification of repeated elements in European pear based on the ‘Rosaceae’ clade from RepBase.</p

Basic statistics on the <i>Pyrus communis</i> ‘Bartlett’ genome sequence.

<p>Figures are given in bp.</p><p>*: the assumed genome size of pear is 600 Mb.</p

Phylogenetic tree of six rosids, four malvids, and three asterids constructed with 83 euKaryote Orthologous Genes (KOGs).

<p>Bootstrap values are listed on each branch. Nodes represent speciation events and branch length represents the degree of evolutional changes over time. The unit for the scale bar at the bottom is nucleotide substitutions per site. The high bootstrap values strongly support that the species in Rosaceae cluster together to the exclusion of any other, and that the European pear and Chinese pear separation event happened after apple speciation.</p

Gene prediction summary for <i>Pyrus communis</i> and comparison with <i>P. bretschneideri</i>, <i>Fragaria vesca</i> and <i>Malus</i>×<i>domestica</i>.

<p>Gene predictions were performed using Augustus for European pear and GeneMark-ES for strawberry. The apple gene models were estimated as the total number of gene predictions minus an estimation of duplications generated by contig overlaps. The redundancy was filtered out using similarity among predictions and positional considerations.</p