For simplicity, we assume that RNA-Seq reads are sequenced uniformly across the transcriptome. In addition, we only consider fixed length single-end RNA-Seq reads. We denote the read length as L. Given a set of MT transcripts, we denote the relative expression levels as τ = (τ1, τ2, . . . , τMT ), the read generating probabilities as Θ = (θ0, θ1, . . . , θMT ) and the expected read coverage as ...

Massive young fruit abscission usually causes low and unstable yield in litchi (Litchi chinensis Sonn.), an important fruit crop cultivated in tropical and subtropical areas. However, the molecular mechanism of fruit drop has not been fully characterized. This study aimed at identification of molecular components involved in fruitlet abscission in litchi, for which reference genome is not avail...

To understand how small mammals cope with the challenge of water homeostasis is a matter of interest for ecologists and evolutionary biologists. Here we take a step towards the understanding of the transcriptomic functional response of kidney using as a model the long-haired mouse (Abrothrix hirta) a species that distributes across Patagonian steppes and Austral temperate rainforests in Argenti...

Wool is produced via synthetic processes of wool follicles, which are embedded in the skin of sheep. The development of new-generation sequencing and RNA sequencing provides new approaches that may elucidate the molecular regulation mechanism of wool follicle development and facilitate enhanced selection for wool traits through gene-assisted selection or targeted gene manipulation. We performed...

We present a de novo assembly of a eukaryote transcriptome using 454 pyrosequencing data. The Glanville fritillary butterfly (Melitaea cinxia; Lepidoptera: Nymphalidae) is a prominent species in population biology but had no previous genomic data. Sequencing runs using two normalized complementary DNA collections from a genetically diverse pool of larvae, pupae, and adults yielded 608,053 expre...

3 Zhongxian Xu, Hang Jie, Binlong Chen, Uma Gaur 1 , Mingyao Yang 1 , Nan Wu 1 , 4 Jian Gao, Pinming Li, Guijun Zhao, Dejun Zeng and Diyan Li 5 1 Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan 6 Province, Sichuan Agricultural University, Chengdu, China 7 2 Laboratory of Medicinal Animal, Chongqing Institute of Medicinal Plant Cultivation, Nanchuan, 8 Chongqin...

This work presents an updated and more complete version of the transcriptome a long-distance migrant, Northern Wheatear (Oenanthe oenanthe). The improved was produced from independent mRNA sequencing adipose tissue, brain, intestines, liver, skin, muscle tissues sampled during autumnal migratory season. new has better coverage is representative species’ phenotype. We assembled 20,248 transcript...

MOTIVATION DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driv...

The Squash bug, Anasa tristis (De Geer), is a major piercing/sucking pest of cucurbits, causing extensive damage to plants and fruits, and transmitting phytopathogens. No genomic resources to facilitate field and laboratory studies of this pest were available; therefore the first de novo exome for this destructive pest was assembled. RNA was extracted from insects challenged with bacterial and ...

Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames (smORFs). The discovery of many smORFs reveals a blind spot in traditional gene-fin...