The Peruvian creole cattle (PCC) is a neglected breed and an essential livestock resource in the Andean region of Peru. To develop modern breeding program conservation strategies for PCC, better understanding genetics this needed. We sequenced whole genome PCC using de novo assembly approach with paired-end 150 strategy on Illumina HiSeq 2500 platform, obtaining 320 GB sequencing data. A refere...

Vibriosis disease by Vibrio spp. greatly reduced productivity of aquaculture, such as brown-marbled grouper (Epinephelus fuscoguttatus), which is an economically important fish species in Malaysia. Preventive measures and immediate treatment are critical to reduce the mortality of E. fuscoguttatus from vibriosis. To investigate the molecular mechanisms associated with immune response and host-b...

SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto ...

UNLABELLED PREMISE OF THE STUDY We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing. Our approach can be used to generate templates from any DNA source for next-generation sequencing. Here we test our approach by amplifying complete chloroplast genomes, and we present a set of 58 potentially universal primers for angiosper...

Spermatonial stem cells (SSCs) are the foundation of spermatogenesis. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with at least 200 bp in length, which play important roles in various biological processes. Growth factor glial cell line-derived neurotrophic factor (GDNF), secreted from testis niches, is critical for self-renewal of SSCs in vitro and in vivo. Using Illumina HiSe...

The sea cucumber (Apostichopus japonicus) occupies a basal position during the evolution of deuterostomes and is also an important aquaculture species. In order to identify more immune effectors, transcriptome sequencing of A. japonicus coelomocytes in response to lipopolysaccharide (LPS) challenge was performed using the Illumina HiSeq™ 2000 platform. One hundred and seven differentially expre...

Ramie (Boehmeria nivea (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems wa...

Circular transcriptome sequencing of the middle silk gland (MSG) and posterior silk gland (PSG) in the Bombyx mori are presented. The middle silk gland and posterior silk gland were collected from the third day of fifth-instar B.mori larvae. The circular RNAs enriched by using RNase R to degrade the linear RNA molecules, and circular RNA sequencing (circRNA-seq) was performed using an Illumina ...

BACKGROUND The tremendous output of massive parallel sequencing technologies requires automated robust and scalable sample preparation methods to fully exploit the new sequence capacity. METHODOLOGY In this study, a method for automated library preparation of RNA prior to massively parallel sequencing is presented. The automated protocol uses precipitation onto carboxylic acid paramagnetic be...