Distribution of molecular subtypes in TMBC patients.

<p>Abbreviation: TMBC, typical medullary breast cancer; ER, estrogen receptor; PR, progesterone receptor; HER-2 IHC, human epidermal growth factor receptor-2immunohistochemistry.</p><p>Distribution of molecular subtypes in TMBC patients.</p

Clinicopathologic characteristics of different molecular subtypes in TMBC patients.

<p>*Difference exists between subgroups; Luminal vs. Triple-negative, MD (Mean Difference)  = 7.55, P = 0.002. Luminal vs. HER-2 overexpression, MD = 4.05, P = 0.212. Luminal vs. Unknown, MD = 1.61, P = 0.689. Triple-negative vs. HER-2 overexpression, MD = −3.50, P = 0.258. Triple-negative vs. Unknown, MD = −5.94, P = 0.129. HER-2 overexpression vs. Unknown, MD = −2.44, P = 0.583.</p><p>Clinicopathologic characteristics of different molecular subtypes in TMBC patients.</p

Histopathological features of TMBC.

<p>(A) Typical syncytial growth pattern of TMBC, with high-grade nuclear atypia (white arrow); ×400. (B) Pushing margin of TMBC (white arrow) and dense lymphoplasmacytic infiltration (black arrow); ×200.</p

<i>De novo</i> Sequence Assembly and Characterization of <i>Lycoris aurea</i> Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing

<div><p>Background</p><p><i>Lycoris aurea</i>, also called Golden Magic Lily, is an ornamentally and medicinally important species of the Amaryllidaceae family. To date, the sequencing of its whole genome is unavailable as a non-model organism. Transcriptomic information is also scarce for this species. In this study, we performed <i>de novo</i> transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for <i>L. aurea</i> using high-throughput sequencing technology.</p><p>Methodology and Principal Findings</p><p>Total RNA was isolated from leaves with sodium nitroprusside (SNP), salicylic acid (SA), or methyl jasmonate (MeJA) treatment, stems, and flowers at the bud, blooming, and wilting stages. Equal quantities of RNA from each tissue and stage were pooled to construct a cDNA library. Using 454 pyrosequencing technology, a total of 937,990 high quality reads (308.63 Mb) with an average read length of 329 bp were generated. Clustering and assembly of these reads produced a non-redundant set of 141,111 unique sequences, comprising 24,604 contigs and 116,507 singletons. All of the unique sequences were involved in the biological process, cellular component and molecular function categories by GO analysis. Potential genes and their functions were predicted by KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literatures, many putative genes involved in Amaryllidaceae alkaloids synthesis, including <i>PAL</i>, <i>TYDC OMT</i>, <i>NMT</i>, <i>P450</i>, and other potentially important candidate genes, were identified for the first time in this <i>Lycoris</i>. Furthermore, 6,386 SSRs and 18,107 high-confidence SNPs were identified in this EST dataset.</p><p>Conclusions</p><p>The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in <i>L. aurea</i>. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will provide useful information for functional genomic research in future.</p></div

Gene Ontology (GO) terms for the transcriptomic sequences of <i>L. aurea</i>.

<p>Gene Ontology (GO) terms for the transcriptomic sequences of <i>L. aurea</i>.</p

Length distribution of <i>L. aurea</i> transcriptomic ESTs. (A) total transcriptomic reads, (B) contigs, (C) singletons.

<p>Length distribution of <i>L. aurea</i> transcriptomic ESTs. (A) total transcriptomic reads, (B) contigs, (C) singletons.</p

Clusters of orthologous groups (COG) classifications of unique <i>L. aurea</i> sequences.

<p>Clusters of orthologous groups (COG) classifications of unique <i>L. aurea</i> sequences.</p

Selected genes of interest for Amaryllidaceae-type alkaloids biosynthesis in the <i>L. aurea</i> transcriptome, including the contigs and singletons.

<p>Selected genes of interest for Amaryllidaceae-type alkaloids biosynthesis in the <i>L. aurea</i> transcriptome, including the contigs and singletons.</p

Distribution of putative single nucleotide polymorphisms (SNP) in the transcriptome of <i>L. aurea</i>.

<p>Distribution of putative single nucleotide polymorphisms (SNP) in the transcriptome of <i>L. aurea</i>.</p

Comparative Genome Analyses of <i>Serratia marcescens</i> FS14 Reveals Its High Antagonistic Potential

<div><p><i>S</i>. <i>marcescens </i>FS14 was isolated from an <i>Atractylodes macrocephala Koidz </i>plant that was infected by <i>Fusarium oxysporum</i> and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the <i>Serratia</i> genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some <i>Serratia</i> species. Comparative analysis further identified that <i>S</i>. <i>marcescens</i> FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in <i>Serratia</i> spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium <i>Ralstonia solanacearum</i> and fungi <i>Fusarium oxysporum </i>and <i>Sclerotinia sclerotiorum</i> were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.</p></div