Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species

Abstract

BackgroundStudying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Ambient), and beyond (Below Ambient and Above Ambient) the altitudinal range limit of species. We sequenced nine transcriptomes (three each from each altitudinal range condition) using Illumina sequencing technology. We compared the fitness variation of transplants among three transplant conditions.ResultsA large number of significantly differentially expressed genes (DEGs) between below ambient versus ambient (109) and above ambient versus ambient (85) were identified. Transcripts involved in plant growth and development were mostly up-regulated in below ambient conditions. Transcripts involved in signalling, defence, and membrane transport were mostly up-regulated in above ambient condition. Pathway analysis revealed that most of the genes involved in metabolic processes, secondary metabolism, and flavonoid biosynthesis were differentially expressed in below ambient conditions, whereas most of the genes involved in photosynthesis and plant hormone signalling were differentially expressed in above ambient conditions. In addition, we observed higher reproductive fitness in transplant individuals at below ambient condition compared to above ambient conditions; contrary to what we expect from the cold adaptive P. sikkimensis plants.ConclusionsWe reveal P. sikkimensis’s capacity for rapid adaptation to climate change through transcriptome variation, which may facilitate the phenotypic plasticity observed in morphological and life history traits. The genes and pathways identified provide a genetic resource for understanding the temperature stress (both the hot and cold stress) tolerance mechanism of P. sikkimensis in their natural environment.

Comparative transcriptomics of sevenImpatiensspecies

“…We annotated more than 73 000 genes for each species, which is comparable with I. walleriana result (70 190). Our results are also comparable with other genera in Ericales order such as Primula (67 201 genes, (66)), Phlox (59 994 genes, (71)), Saltugilia (51 020-92 672 genes,(72)), Camellia (46 223-46 736, (73)) and Vaccinium (35 060 – 67 836 genes (74, 75). GO terms assignment for identified transcripts is surprisingly similar between\ species.…”

“…Our results suggest that species within this genus transcribe similar sets of genes and potential differences can be pronounced in differential expression of these genes or their sequence. Similar results were published by Gurung et al (66), who studied species plasticity by comparison of transcriptome size in Primula sikkimensis and they identified 21 167 transcripts and 109 and 85 genes which were differentially expressed between three altitudinal positions in which the plants were cultivated.…”

“…They described from 2 879 to 7 185 seasonally oscillating genes. Gurung et al (66) compared transcriptome size in a Himalaya plant ( Primula sikkimensis ) growing along an altitudinal gradient and carried out a transplant experiment within the altitudinal gradient. Total number of transcribed genes fluctuated between 38 423 and 48 674 depending on altitude of plant cultivation, which reflects species plasticity rather than adaptation.…”

Altitudinal variation in phytochemical, physicochemical, and morphological aspects of Justicia adhatoda L. plant growing wildly in Western Himalayas

“…In a study done on Adhatoda zeylanica in different phytogeographical regions of South India, four distinctive morphotypes were identified based and they exhibited significant variation in quantitative their vasicine content [26]. Plants may counter multiple stress conditions in various ways [27]. Explicitly, the plants are challenged to fight surplus abiotic and biotic stresses operating at different elevations and the worthwhile adaptation of plants to their sessile lifestyle can be ascribed to their capability to adapt and respond to various types of stresses.…”

Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex

“…The flavonoid biosynthetic pathway leading to accumulation of anthocyanins is highly conserved and well characterized, and has been extensively studied in many species, most of which are in model plants or agriculturally and horticulturally important plants [12][13][14][15]. Few studies have examined the molecular basis underlying the formation and accumulation of anthocyanin in wild species [16,17]. Based on these studies, three major associated factors have been proposed to be involved in anthocyanin accumulation, including transcription regulatory genes (MYB-bHLH-WD40 complex) that occur in the nucleus, structural genes (CHS, FLS, DFR, ANS) acting in the biosynthetic pathway, and transporter genes (GST) transferring anthocyanin from the cytosol into the vacuole [10,18,19].…”