A whole-transcriptome approach to evaluate reference genes for quantitative diurnal gene expression studies under natural field conditions in Tamarix ramosissima leaves

Background: Tamarix ramosissima is a desert forest tree species that is widely distributed in the drought-stricken areas to sustain the fragile ecosystem. Owing to its wide usage in the desert restoration of Asia, it can be used as an ecophysiological model plant. To obtain reliable and accurate results, a set of reference genes should be screened before gene expression. However, up to date, systematical evaluation of reference genes has not been conducted in T. ramosissima. Results: In this study, we used eigenvalues derived from principal component analysis to identify stable expressed genes from 72,035 unigenes from diurnal transcriptomes under natural field conditions. With combined criteria of read counts above 900 and CV of FPKM below 0.3, a total of 7385 unigenes could be qualified as candidate reference genes in T. ramosissima. By using three statistical algorithm packages, geNorm, NormFinder, and BestKeeper, the stabilities of these novel reference genes were further compared with a panel of traditional reference genes. The expression patterns of three aquaporins (AQPs) suggested that at least UBQ (high expression), EIF4A2 (low expression), and GAPDH (moderate expression) could be qualified as ideal reference genes in both RT-PCR and RNA-seq analysis of T. ramosissima. Conclusions: This work will not only facilitate future studies on gene expression and functional analysis of genetic resources of desert plants but also improve our understanding of the molecular regulation of water transport in this plant, which could provide a new clue to further investigate the drought adaptation mechanism of desert plant species under harsh environments.

Notas sobre Chloraea undulata "Orquídea de Lima" y su registro en las lomas de Asia, Cañete, Perú

Chloraea undulata es una orquídea endémica del Perú. Originalmente colectada por Antonio Raimondi en el siglo XIX, fué reconocida como una especie característica de las lomas de Lima hasta mediados del siglo pasado. Desde entonces, la especie ha sido considerada desaparecida de las lomas costeras y especialmente del Cerro Amancaes, su localidad tipo, que hoy integra el casco urbano de la capital. En el presente trabajo, se documenta su presencia en las lomas de Asia 100 km al sur de Lima y se valora la importancia de este hallazgo para la conservación de la especie y su hábitat.

Chloraea undulata is an orchid endemic to Peru. Originally collected by Antonio Raimondi in XIX century, until first half of the last century it has been regarded as a species characteristic of the hills around Lima. The "Lima orchid" Chloraea undulata is considered to be in decline in the hills of Lima province, especially in the type localities of Cerro Amancaes and Cerro El Agustino where urban growth and expansion has been significant. In this paper its presence in the hills of Asia District, 100 km south of Lima, is documented, and we also analyzed the implications of this finding for the species conservation and their habitat.