Dataset Information

Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts.

ABSTRACT: Rheum nobile is an alpine plant with translucent bracts concealing the inflorescence which produce a "glasshouse" effect promoting the development of fertile pollen grains in such conditions. The current understanding of the adaptation of such bracts to alpine environments mainly focuses on the phenotypic and physiological changes while the genetic basis is very limited. By sequencing the upper bract and the lower rosulate leaf from the same R. nobile stem, we identified candidate genes that may be involved in alpine adaption of the translucent bract in "glasshouse" plants and illustrated the changes in gene expression underlying the adaptive and complex evolution of the bracts phenotype.A total of 174.2 million paired-end reads from each transcriptome were assembled into 25,249 unigenes. By comparing the gene expression profiles, we identified 1,063 and 786 genes up-regulated respectively in the upper bract and the lower leaf. Functional enrichment analyses of these genes recovered a number of differential important pathways, including flavonoid biosynthesis, mismatch repair and photosynthesis related pathways. These pathways are mainly involved in three types of functions: 9 genes in the UV protective process, 9 mismatch repair related genes and 88 genes associated with photosynthesis.This study provides the first comprehensive dataset characterizing Rheum nobile gene expression at the transcriptomic scale, and provides novel insights into the gene expression profiles associated with the adaptation of the "glasshouse" plant bracts. The dataset will be served as a public genetic resources for further functional and evolutionary studies of "glasshouse" plants.

SUBMITTER: Wang L

PROVIDER: S-EPMC4208811 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts.

Wang Lizhong L Zhou Haihong H Han Jin J Milne Richard I RI Wang Mingyu M Liu Bingbing B

PloS one 20141024 10

<h4>Background</h4>Rheum nobile is an alpine plant with translucent bracts concealing the inflorescence which produce a "glasshouse" effect promoting the development of fertile pollen grains in such conditions. The current understanding of the adaptation of such bracts to alpine environments mainly focuses on the phenotypic and physiological changes while the genetic basis is very limited. By sequencing the upper bract and the lower rosulate leaf from the same R. nobile stem, we identified candi ...[more]

PMID: 25343261

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Project description:BackgroundPerennity of giant rosette species in combination with a single 'big bang' reproduction followed by death of the genetic individual is relatively rare among plants. Such long-lived monocarpic plants are usually slow growing and can be found in deserts, bogs or in alpine regions of the tropics or sub-tropics. Due to their longevity, monocarpic perennials risk losing everything before reproduction, which make them particularly susceptible to disturbances. Because of the inherent difficulties in assessing whether long-lived populations are growing or declining, usually neither their demography nor the consequences of increasing grazing pressure are known.MethodsWe used integral projection modelling (IPM) to measure the growth rate and passage time to flowering of Rheum nobile, a monocarpic perennial, and one of the most striking alpine plants from the high Himalayas. Rosettes which were no longer found due to disturbances or grazing by yaks were either treated as missing or as dead in two series of analysis, thereby simulating demography with and without the impact of grazing cattle. Data were collected from plants at 4500 m a.s.l. in Shangri-la County, Yunnan Province, south-west China. In four consecutive years (2011-2014) and in two populations, 372 and 369 individuals were measured, respectively, and size-dependent growth, survival and fecundity parameters were estimated. In addition, germination percentage, seedling survival and establishment probability were assessed.Key resultsThe probability of survival, flowering and fecundity were strongly size dependent. Time to reach flowering size was 33.5 years [95 % confidence interval (CI) 21.9-43.3, stochastic estimate from pooled transitions and populations]. The stochastic population growth rate (λs) of Rheum nobile was 1.013 (95 % CI 1.010-1.017). When disturbance by grazing cattle (yaks) was accounted for in the model, λs dropped to values <1 (0.940, 95 % CI 0.938-0.943).ConclusionWe conclude that natural populations of this unique species are viable, but that conservation efforts should be made to minimize disturbances by grazing and to protect this slow-growing flagship plant from the high Himalayas.

Dataset Information

Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts.

Publications

Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts.

Similar Datasets

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