De Novo Discovery and Comparison of Transposable Element Families in S. lycopersicum and S. pimpinellifolium

<p>Solanum lycopersicum has fewer high-copy, full-length long terminal repeat (LTR) retrotransposons than Arabidopsis and sorghum, and the average insertion age is older (2.8 vs 0.8 mya). Tandem repeat families, telomeric repeats and other repeats are found in centromeres, telomeres and other heterochromatic regions. Transposable elements (TEs) are found in both heterochromatin and euchromatin. There is a lack of well characterized repeat libraries for Solanaceous species compared to grasses like rice and wheat.</p> <p>The transposable elements in the domesticated tomato genome, S. lycopersicum heinz 1706, will be compared to S. pimpinellifolium (a close wild ancestor to domesticated tomato) as well as other more distant wild relatives and heirloom varieties and characterized by</p> <p>•Copy number</p> <p>•Within-family sequence similarity</p> <p>•Indels in alignments</p> <p>The identified transposable elements will be catalogued and available through the Sol Genomics network (SGN, http://solgenomics.net/), a clade oriented database and a repository for a large and growing number of solanaceae genomes. The collection of genomic data and computational resources of SGN provides the opportunity to study TEs across a phenotypically diverse and economically important plant family.</p

Hoyt_ACPmetagenomicsPosterSummer2017.pdf

<div>Citrus greening disease, or Huanglongbing (HLB) has infected citrus trees around the world. HLB is associated with the bacterium ‘<i>Candidatus</i> Liberibacter asiaticus’ (CLas), and is transmitted by <i>Diaphorina citri</i>, also known as the Asian citrus psyllid (ACP) [1]. ACP is known to have the endosymbionts Wolbachia, Carsonella, and Profftella, and it is possible that other bacteria are associated with the ACP at lower abundance. The objective of this project is to utilize metagenomic pipelines in order to analyze whole-body ACP DNA sequences for differences in taxonomy and abundance of endosymbionts. </div><div><br></div

Taxonomic Analysis of the Endosymbionts in the Asian Citrus Psyllid through Metagenomics

<div>Citrus greening disease, or Huanglongbing (HLB) has infected citrus trees around the world. HLB is associated with the bacterium ‘<i>Candidatus </i>Liberibacter asiaticus’ (CLas), and is transmitted by <i>Diaphorina citri</i>, also known as the Asian citrus psyllid (ACP) [1]. ACP is known to have the endosymbionts Wolbachia, Carsonella, and Profftella, and it is possible that other bacteria are associated with the ACP at lower abundance. The objective of this project is to utilize metagenomic pipelines in order to analyze whole-body ACP DNA sequences for differences in taxonomy and abundance of endosymbionts. </div><div><br></div

Additional file 9: Figure S8. of Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

The age of the genes specific to each genomic region. Counting genes considering their phylogenetic origin and comparing that repartition to that expected give us an information about gene age repartition in the three compartments. Statistical analyzes (chi-square tests) were conducted to validate the observations and are represented by the P-value on this graphic. (TIF 130 kb

Petasites fragrans Presl

原著和名: ニホヒクヮントウ科名: キク科 = Compositae採集地: 千葉県 船橋市三山2-2-1 東邦大学 (下総 東邦大学)採集日: 1972/3/1採集者: 萩庭丈壽整理番号: JH007510国立科学博物館整理番号: TNS-VS-95751

Additional file 4: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Table S7. Complete RNA seq data. (TXT 9489 kb

Additional file 1: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Table S1. Sequence Summary Statistics. Table S2. Differentially expressed genes between Sue 1 and Sue 16. Homoeologs are indicated in matching color pairs. Table S3. Enriched Gene Ontology Categories in 148 Differentially Expressed Genes. Analysis was performed using topGO in R (Alexa and Rahnenfuhrer [36]). P-values are from Fisher’s Exact Test under a weighted model (Alexa et al. [37]). We further categorized the GO categories into either biotic stress response, abiotic stress response, general stress response (both biotic and abiotic), or not stress related categories. Table S4. Observed SNP distribution in DEGs and non-differentially expressed genes. Total basepairs (bps) in coding sequence (CDS) in the bottom right cell came from the A. thaliana CDS FASTA file. Of those, 155,619 bps fall in differentially expressed genes (DEGs). Our analysis found 71,636 SNPs between Sue 1 and Sue 16,203 of which fall in DEGs. We performed a chi-square analysis and got a p-value of .32 indicating there is no difference from the expected distribution if SNPs fell randomly in all genes. Table S5. SNPs in Sue 1, Sue 16, and the 1001 genomes database. Table S6. Comparison of Sue 1 and Sue 16 SNPs to ecotypes in the 1001 genomes database using SNPmatch. (XLSX 36 kb

Additional file 2: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Figure S1. Members of the xyloglucan transglycosylase/hydrolase (XTH) family are significantly differentially upregulated in Sue 16 relative to Sue 1. Shown are FPKM expression values with confidence intervals from Cuffdiff analysis for both homoeologs of XTH4 and XTH22. (PDF 471 kb

Additional file 5: Figure S4. of Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L)

Principal Component Analysis of the first three components representing 21.3 % of total variation of the cape gooseberry SNP markers obtained after comparisons with the: (a) cape gooseberry transcriptome (1,699 SNPs), (b) potato reference genome (1,695 SNPs) and (c) tomato reference genome (1,739 SNPs). (PDF 73 kb

Additional file 1: Table S1. of Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L)

List of the germplasm used for association of the cape gooseberry resistance response to F. oxysporum in the present study. (XLS 50 kb