High-throughput sequencing of the frog Xenopus tropicalis, utilizing the Genome Analyzer, helped find two novel micro (mi) RNAs and piRNAs in the female germline, and miRNAs and siRNAs in somatic tissue. It was postulated that at least some of the small RNAs are involved in silencing of repetitive elements.

The authors analyzed and compared microRNAs (miRNAs) in the temperate grass Brachypodium distachyon. Using deep sequencing technology on the Genome Analyzer, the authors identified 23 novel miRNAs in Chinese Spring wheat and 94 conserved and one novel miRNA in Brachypodium. They also investigated miRNA expression levels and found differences between Brachypodium tissue types (vegetative and reproductive) and between the two plant types for some mRNAs, particularly one involved in control of lignin metabolism.

The authors used high-throughput parallel sequencing, on the Genome Analyzer, of small interfering RNAs (siRNAs) to identify both known and unknown RNA and DNA viruses infecting sweet potato plants. These included RNA, ssDNA, and dsDNA reverse transcribing viruses. They also reconstruct the entire genome of sweet potato feathery mottle virus (SPFMV).

Piwi-interacting RNAs (piRNAs) are transposon silencers that act as guides for a subfamily of Argonaute proteins—PIWI proteins—expressed in germline cells. The authors used flies with ago3 loss-of-function mutations to show that Ago3 increases levels of these piRNAs. The also show a separate, simpler, somatic, piRNA pathway that does not rely on Ago3 amplification. They used the Genome Analyzer for small RNA sequencing.