Supplemental Material for Sweet et al., 2022

Assemblies, annotations, output files, and control files involved in the assembly and annotation of the genome of Brueelia nebulosa, including the mitogenome and genome from the primary endosymbiont. The files include GFF annotation files for the Brueelia genome and primary endosymbiont, control file for the MAKER pipeline, output files from PSMC, and gene cluster lists and functions generated from Orthovenn.</p

Identification of Tomato necrotic stunt virus (ToNSV) in the Mexican sample (MX) and its relationship with other viruses in the family of Potyviridae.

<p>A. Relative placement of <i>de novo</i> assembled siRNA contigs onto a general potyvirus genome. B. Distribution of siRNAs along the ToNSV genome in both (+) and (−) polarities. C. Phylogenetic relationship of the newly identified ToNSV genome in relationship to other viruses in the family of Potyviridae. The full name of potyviruses and their respective GenBank accession numbers are: ToNSV-MX9354: JQ314463; PTMV, <i>Peru tomato mosaic virus</i>: AJ516010; PVY-O, <i>Potato virus Y</i>: HQ912914; PeSMV, <i>Pepper severe mosaic virus</i>: AM181350; PeMoV, <i>Pepper mottle virus</i>: EU586135; PVV, Potato virus V: NC_004010; PepYMV, <i>Pepper yellow mosaic virus</i>: NC_014327; BiMoV, <i>Bidens mottle virus</i>: EU250214; WMV, <i>Watermelon mosaic virus</i>: DQ399708; PVMV, <i>Pepper veinal mottle virus</i>: FM202327; TVBMV, <i>Tobacco vein-banding mosaic virus</i>: EF219408; TVMV, <i>Tobacco vein mottling virus</i>: X04083; and TEV, <i>Tobacco etch virus</i>: EF470242. SPMMV, <i>Sweet potato mild mottle virus</i>: NC_003739, genus <i>Ipomovirus</i>, was used as an outgroup sequence to anchor the phylogenetic tree.</p

Profiling of siRNAs along the respective strains of <i>Pepino mosaic virus</i> in three U.S. tomato samples.

<p>CAHN8: top panels <b>A</b> and <b>B</b>; EF09-58: middle panels <b>C</b> and <b>D</b>; and EF09-60: bottom panels <b>E</b> and <b>F</b>. Red lines above the model PepMV genome structures depict broken coverage by either sense or antisense siRNAs. The hot spot for each PepMV isolate is indicated with an arrow.</p

Small RNA (sRNA) profiles in four suspect virus-infected tomato samples.

<p><b>A</b>. Enrichment of a virus-like siRNA pool through subtraction of host tomato sRNAs. <b>B</b>. Enriched virus-like sRNAs matching known virus and viroid genomes. <b>C</b>. Size distribution of total sRNAs (from 15 to 36 nt) in the four samples. <b>D</b>. After subtracting host sRNAs, size distribution of siRNAs in each library against respective virus and viroid.</p

Validation and confirmation of the siRNA derived sequences of two strains of <i>Pepino mosaic virus</i> through Sanger sequencing.

<p>A. A general PepMV genome organization includes RNA-dependant RNA polymerase (RDRP), triple gene block (TGB) 1, 2 and 3, and coat protein (CP). B. Schematic presentation of step-wise overlapping RT-PCR products generated for sequence confirmation. C. Example of RT-PCR products generated using the US1 strain-specific primers. D. Example of RT-PCR products generated using the EU strain specific primers. M is a DNA ladder with 300, 500, 750 and 1000 bp, respectively. E. Phylogenetic relationship of <i>Pepino mosaic virus</i> isolates generated with full genomic sequences showing the newly characterized isolates (EF09-58, EF09-60 and CAHN8) are closely related to the EU or US1 genotypes. The isolates of PepMV and their respective GenBank accession numbers, PepMV-EU_CAHN8: JQ314457; PepMV-US1_CAHN8: JQ314458; PepMV-EU_EF09-58,JQ314459; PepMV-US1_EF09-58: JQ314460; PepMV-EU_EF09-60: JQ314461; PepMV-US1_EF09-60: JQ314462; PepMV-P22: HQ650560; PepMV-PK: EF408821; PepMV-P19: HQ650559; PepMV-Pa: FJ612601; PepMV-UK: FJ212288; PepMV-SIC1-09: HQ663891; PepMV-SIC2-09: HQ663892; PepMV-SAR01: HQ663893; PepMV-Ch2: DQ000985; PepMV-SAR09: HQ663890; PepMV-US2: AY509927; PepMV-US1-NL: FJ940225; PepMV-Ch1: DQ000984; PepMV-US1: AY509926; PepMV-EU-France: AJ438767; PepMV-Sp-13: AF484251; PepMV-LE-2000: AJ606359; PepMV-LE-2002: AJ606360; PepMV-P11: JN133846; PepMV-EU-Tomato: FJ940223; PepMV-DB1: FJ940224; PepMV-LP-2001: AJ606361, and PepMV-SM.74: AM109896.</p

Ratio of virus (+) and (−) polarity siRNAs and hotspots in <i>Potato spindle tuber viroid</i> A.

<p>Ratio of (+) and (<b>−</b>) polarity siRNA reads for PSTVd and both stains of PepMV (EU and US1) in the three U.S. tomato samples. <b>B</b>. Distribution of siRNAs along the <i>Potato spindle tuber viroid</i> (PSTVd) genome in both (+) and (<b>−</b>) polarities.</p

Detection and Validation of QTL Affecting Bacterial Cold Water Disease Resistance in Rainbow Trout Using Restriction-Site Associated DNA Sequencing

<div><p>Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellite markers in a genome scan, we previously detected significant and suggestive QTL affecting phenotypic variation in survival following challenge with <i>Flavobacterium psychrophilum</i>, the causative agent of BCWD in rainbow trout. In this study, we performed selective genotyping of SNPs from restriction-site associated DNA (RAD) sequence data from two pedigreed families (2009070 and 2009196) to validate the major QTL from the previous work and to detect new QTL. The use of RAD SNPs in the genome scans increased the number of mapped markers from ~300 to ~5,000 per family. The significant QTL detected in the microsatellites scan on chromosome Omy8 in family 2009070 was validated explaining up to 58% of the phenotypic variance in that family, and in addition, a second QTL was also detected on Omy8. Two novel QTL on Omy11 and 14 were also detected, and the previously suggestive QTL on Omy1, 7 and 25 were also validated in family 2009070. In family 2009196, the microsatellite significant QTL on Omy6 and 12 were validated and a new QTL on Omy8 was detected, but none of the previously detected suggestive QTL were validated. The two Omy8 QTL from family 2009070 and the Omy12 QTL from family 2009196 were found to be co-localized with handling and confinement stress response QTL that our group has previously identified in a separate pedigreed family. With the currently available data we cannot determine if the co-localized QTL are the result of genes with pleiotropic effects or a mere physical proximity on the same chromosome segment. The genetic markers linked to BCWD resistance QTL were used to query the scaffolds of the rainbow trout reference genome assembly and the QTL-positive scaffold sequences were found to include 100 positional candidate genes. Several of the candidate genes located on or near the two Omy8 QTL detected in family 2009070 suggest potential linkages between stress response and the regulation of immune response in rainbow trout.</p></div

Plasma Exosomal miRNAs in Persons with and without Alzheimer Disease: Altered Expression and Prospects for Biomarkers

<div><p>To assess the value of exosomal miRNAs as biomarkers for Alzheimer disease (AD), the expression of microRNAs was measured in a plasma fraction enriched in exosomes by differential centrifugation, using Illumina deep sequencing. Samples from 35 persons with a clinical diagnosis of AD dementia were compared to 35 age and sex matched controls. Although these samples contained less than 0.1 microgram of total RNA, deep sequencing gave reliable and informative results. Twenty miRNAs showed significant differences in the AD group in initial screening (miR-23b-3p, miR-24-3p, miR-29b-3p, miR-125b-5p, miR-138-5p, miR-139-5p, miR-141-3p, miR-150-5p, miR-152-3p, miR-185-5p, miR-338-3p, miR-342-3p, miR-342-5p, miR-548at-5p, miR-659-5p, miR-3065-5p, miR-3613-3p, miR-3916, miR-4772-3p, miR-5001-3p), many of which satisfied additional biological and statistical criteria, and among which a panel of seven miRNAs were highly informative in a machine learning model for predicting AD status of individual samples with 83–89% accuracy. This performance is not due to over-fitting, because a) we used separate samples for training and testing, and b) similar performance was achieved when tested on technical replicate data. Perhaps the most interesting single miRNA was miR-342-3p, which was a) expressed in the AD group at about 60% of control levels, b) highly correlated with several of the other miRNAs that were significantly down-regulated in AD, and c) was also reported to be down-regulated in AD in two previous studies. The findings warrant replication and follow-up with a larger cohort of patients and controls who have been carefully characterized in terms of cognitive and imaging data, other biomarkers (e.g., CSF amyloid and tau levels) and risk factors (e.g., apoE4 status), and who are sampled repeatedly over time. Integrating miRNA expression data with other data is likely to provide informative and robust biomarkers in Alzheimer disease.</p></div

Rainbow trout genome scaffolds [22] matched by markers linked to BCWD resistance QTL.

<p>^a In family 2009070 on Omy7 and 8 we have identified two QTL. Omy7 QTL-1 and -2 are located on cM 54 and 142, respectively. Omy8 QTL-1 and -2 are located on cM 47 and 88, respectively. GWAS notation near the Omy number means that the marker was detected through genome-wide association analysis.</p><p>Rainbow trout genome scaffolds [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138435#pone.0138435.ref022" target="_blank">22</a>] matched by markers linked to BCWD resistance QTL.</p

QTL for BCWD resistance detected and validated using outbred population (TREE Model) analysis in two rainbow trout families for the phenotypes survival days (Days) and survival status (Status).

<p>^a N = 120 offspring genotyped in each family with 1,167 and 1,348 mapped markers (microsatellites and RAD SNPs) in families 2009070 and 2009196, respectively.</p><p>^b Only QTL found to be significant in the current study are listed (<i>P</i>_{<i>GenomeWide</i>}<0.05).</p><p>^c QTL was previously detected as significant, suggestive or not detected in this family using microsatellites only [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138435#pone.0138435.ref004" target="_blank">4</a>].</p><p>QTL for BCWD resistance detected and validated using outbred population (TREE Model) analysis in two rainbow trout families for the phenotypes survival days (Days) and survival status (Status).</p