Unigene homology searches against the NR database.

<p>(A) The E-value distribution of BLAST hits for the assembled unigenes in the NR database. (B) The similarity distribution of BLAST hits against the NR database for each unigene. (C) Species distribution of the top BLASTx hits against the NR database for each unigene.</p

Summary of the Chinese chive transcriptome sequencing using the Illumina HiSeq.

<p>Summary of the Chinese chive transcriptome sequencing using the Illumina HiSeq.</p

<i>De Novo</i> Assembly and Annotation of the Chinese Chive (<i>Allium tuberosum</i> Rottler ex Spr.) Transcriptome Using the Illumina Platform

<div><p>Chinese chive (<i>A</i>. <i>tuberosum</i> Rottler ex Spr.) is one of the most widely cultivated <i>Allium</i> species in China. However, minimal transcriptomic and genomic data are available to reveal its evolution and genetic diversity. In this study, de novo transcriptome sequencing was performed to produce large transcript sequences using an Illumina HiSeq 2000 instrument. We produced 51,968,882 high-quality clean reads and assembled them into 150,154 contigs. A total of 60,031 unigenes with an average length of 631 bp were identified. Of these, 36,523 unigenes were homologous to existing database sequences, 35,648 unigenes were annotated in the NCBI non-redundant (Nr) sequence database, and 23,509 unigenes were annotated in the Swiss-Prot database. A total of 26,798 unigenes were assigned to 57 Gene Ontology (GO) terms, and 13,378 unigenes were assigned to Cluster of Orthologous Group categories. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, we mapped 21,361 unigenes onto 128 pathways. Furthermore, 2,125 sequences containing simple sequence repeats (SSRs) were identified. This new dataset provides the most comprehensive resource currently available for gene expression, gene discovery, and future genomic research on Chinese chive. The sequence resources developed in this study can be used to develop molecular markers that will facilitate further genetic research on Chinese chive and related species.</p></div

Summary of the functional annotation of assembled unigenes.

<p>Summary of the functional annotation of assembled unigenes.</p

GO classification of assembled sequences.

<p>A total of 13,897 unigenes were grouped into three main GO categories: ‘Biological Processes’, ‘Cellular Component’, and ‘Molecular Function’.</p

COG functional classification of unigenes.

<p>A total of 950 assembled unigenes were annotated and assigned to 24 functional categories.</p

Statistics of the SSRs identified in the <i>A</i>. <i>tuberosum</i> transcriptome.

<p>Statistics of the SSRs identified in the <i>A</i>. <i>tuberosum</i> transcriptome.</p

Statistical summary of the de novo transcriptome assembly for <i>A</i>. <i>tuberosum</i> Rottler ex Spr.

<p>Statistical summary of the de novo transcriptome assembly for <i>A</i>. <i>tuberosum</i> Rottler ex Spr.</p

Epigenetic changes at the IGF2-H19 locus in UROtsa cells chronically treated with CSE.

<p>A. Percentage of methylation at 3 CpG sites in the IGF2 DMR determined by bisulfite sequencing of genomic DNA extracted from UROtsa cells chronically treated with CSE, UROCSE-p32 (32^nd passage) and from untreated cells, UROtsa-p32 (32^nd passage). HM: hypermethylated with 3 of 3 CpG sites presenting methylation; IM: intermediately methylated with 2 or 1 of 3 CpG sites presenting methylation; UM: unmethylated with 0 of 3 CpG sites presenting methylation; n = 58 for both UROtsa-p32 and UROCSE-p32. The increase of UM DNA at this locus in the UROCSE-p32 cells was statistically significant (<i>p</i><0.05), as indicated in the figure. B. Percentage of methylation at 23 CpG sites in the H19 CBS6 determined by bisulfite sequencing of genomic DNA extracted from UROtsa cells chronically treated with CSE, UROCSE-p32 (32^nd passage) and from untreated cells, UROtsa-p32 (32^nd passage). HM: hypermethylated with >70% of the CpG sites presenting methylation; UM: unmethylated with 0 of 23 CpG sites presenting methylation; n = 60 for both UROtsa-p32 and UROCSE-p32. One clone presenting 8 methylated CpG sites of the 23 was observed for the UROCSE-p32 cells and was counted as UM. The increase of UM DNA at this locus in the UROCSE-p32 cells was statistically significant (<i>p</i><0.05), as indicated in the figure.</p

Polymerase activity of avian-human viral ribonucleoprotein (RNP) complexes.

<p>(A) A549 cells were transfected in duplicate with pPol1-NS-Renilla and pSV40-Luc reporter plasmids, together with plasmids expressing PB2, PB1, PA and NP from either WY03 (human symbol) or TH04 (chicken symbol) viruses. Cells were incubated at 33°C (hatched bars) or 37°C (solid bars) for 24 hours and cell lysates were analyzed to measure Renilla and firefly luciferase activities. The latter was used to normalize transfection efficiency. Values shown represent the activities of each RNP relative to that of WY03 measured at 37°C (100%). (B) Viral RNP activities derived from WY03 (human symbol) or VN04 (chicken symbol) viruses are shown as described in panel A.</p