Phylogenetic tree of SLC30 family transporters.

<p>The phylogenetic tree was constructed using maximum likelihood algorithm under the JTT+I+G model of amino acid substitution as described in detail in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116043#s4" target="_blank">Materials and Methods</a> section. Numbers around the nodes correspond to bootstrap support values in percentages.</p

Sequencing and <i>De Novo</i> Analysis of the Hemocytes Transcriptome in <i>Litopenaeus vannamei</i> Response to White Spot Syndrome Virus Infection

<div><p>Background</p><p>White spot syndrome virus (WSSV) is a causative pathogen found in most shrimp farming areas of the world and causes large economic losses to the shrimp aquaculture. The mechanism underlying the molecular pathogenesis of the highly virulent WSSV remains unknown. To better understand the virus-host interactions at the molecular level, the transcriptome profiles in hemocytes of unchallenged and WSSV-challenged shrimp (<i>Litopenaeus vannamei</i>) were compared using a short-read deep sequencing method (Illumina).</p><p>Results</p><p>RNA-seq analysis generated more than 25.81 million clean pair end (PE) reads, which were assembled into 52,073 unigenes (mean size = 520 bp). Based on sequence similarity searches, 23,568 (45.3%) genes were identified, among which 6,562 and 7,822 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 14,941 (63.4%) unigenes to 240 KEGG pathways. Among all the annotated unigenes, 1,179 were associated with immune-related genes. Digital gene expression (DGE) analysis revealed that the host transcriptome profile was slightly changed in the early infection (5 hours post injection) of the virus, while large transcriptional differences were identified in the late infection (48 hpi) of WSSV. The differentially expressed genes mainly involved in pattern recognition genes and some immune response factors. The results indicated that antiviral immune mechanisms were probably involved in the recognition of pathogen-associated molecular patterns.</p><p>Conclusions</p><p>This study provided a global survey of host gene activities against virus infection in a non-model organism, pacific white shrimp. Results can contribute to the in-depth study of candidate genes in white shrimp, and help to improve the current understanding of host-pathogen interactions.</p></div

Summary of SLC30 and SLC39 families in common carp genome.

<p>Summary of SLC30 and SLC39 families in common carp genome.</p

Phylogenetic tree of SLC39 family transporters.

<p>The phylogenetic tree was obtained as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116043#pone-0116043-g003" target="_blank">Fig. 3</a>. Numbers around the nodes correspond to bootstrap support values.</p

Saturation analyses of DGE clean reads generated from mock, early infection and late infection samples.

<p>With the number of reads increasing, the number of detected genes is increasing. When the number of reads reaches certain value, the growth rate of detected genes flattens, and it means that the number of detected genes tends to saturation.</p

Annotation of unigenes.

<p>Annotation of unigenes.</p

Schematic representation of the domain architecture of zinc transporters in common carp.

<p>TM represents the transmembrane region; RPT represents the internal repeat 1; BLAST represents the domain present in proteins and involved in regulation of nuclear pre-mRNA; SCOP represents the putative copper-binding protein; DUF4554 represents the domain of unknown function 4554; and Yippee-Mis18 represents the Yippee zinc-binding/DNA-binding/Mis18.</p

RT-PCR based expression analysis of common carp zinc transporter genes.

<p>The amplification of β-actin was used as an internal control. Gene names are indicated on the left of the panel.</p

Comparative analysis of zinc transporters of common carp with other species.

<p>Comparative analysis of zinc transporters of common carp with other species.</p