Dataset Information

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats.

ABSTRACT: Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant Ranunculus bungei, and two terrestrial relatives R. cantoniensis and R. brotherusii, followed by comparative evolutionary analyses to determine candidate genes for adaption to aquatic habitats. We obtained 126,037, 140,218 and 114,753 contigs for R. bungei, R. cantoniensis and R. brotherusii respectively. Bidirectional Best Hit method and OrthoMCL method identified 11,362 and 8,174 1:1:1 orthologous genes (one ortholog is represented in each of the three species) respectively. Non-synonymous/synonymous (dN/dS) analyses were performed with a maximum likelihood method and an approximate method for the three species-pairs. In total, 14 genes of R. bungei potentially involved in the adaptive transition from terrestrial to aquatic habitats were identified. Some of the homologs to these genes in model plants are involved in vacuole protein formation, regulating 'water transport process' and 'microtubule cytoskeleton organization'. Our study opens the door to understand the molecular mechanism of plant adaptation from terrestrial to aquatic habitats.

SUBMITTER: Chen LY

PROVIDER: S-EPMC4438715 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats.

Chen Ling-Yun LY Zhao Shu-Ying SY Wang Qing-Feng QF Moody Michael L ML

Scientific reports 20150520

Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant Ranunculus bungei, and two terrestrial relatives R. cantoniensis and R. brotherusii, followed by comparative evolutionary analyses to determine candidate genes for adaption to aquatic habitats. We obtained 126,037, ...[more]

PMID: 25993393

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Project description:Worldwide, the genus Ranunculus includes approximately 600 species and is highly genetically diverse. Recent taxonomic reports suggest that the genus has a monophyletic origin, divided into two subgenera, and consists of 17 sections. The Central Asian country of Kazakhstan has 62 species of the genus that have primarily been collected in the central part of the country. The latest collection trips in southern parts of the country have led to the description of a wider distribution area for Ranunculus and the identification of a new species Ranunculus talassicus Schegol. et A.L. Ebel from Western Tien Shan. Therefore, in this study, attempts were made to assess the molecular taxonomic positions of R. talassicus and two other species endemic to the Central Asian region R. karkaralensis Schegol. and R. pskemensis V.N. Pavlov in relation to other species of the genus, using internal transcribed spacer (ITS) molecular genetic markers. The ITS-aligned sequences of 22 local Central Asian accessions and 43 accession sequences available in the National Center for Biotechnology Information (NCBI) database allowed the construction of a maximum parsimony phylogenetic tree and a Neighbor-Net network. The results indicated that R. talassicus and R. pskemensis could be assigned to section Ranunculastrum. Additionally, an assessment of the network suggested that R. pskemensis was the rooting taxon for the group of species containing R. talassicus, and that R. illyricus L. and R. pedatus Waldst. & Kit. were founders of a prime rooting node for the Ranunculastrum section of the genus. The ITS-aligned sequences showed that R. karkaralensis was indifferent with respect to three other species in the Ranunculus section of the genus, i.e., R. acris L., R. grandifolius C.A. Mey., and R. subborealis Tzvelev. The study indicated that the assessments of ITS-based phylogenetic tree and Neighbor-Net network provided new insights into the taxonomic positions of three endemic species from Central Asia.

Project description:The globally distributed green microalga Chlorella vulgaris (Chlorophyta) colonizes aquatic and terrestrial habitats, but the molecular mechanisms underpinning survival in these two contrasting environments are far from understood. Here, we compared the authentic strain of C. vulgaris from an aquatic habitat with a strain from a terrestrial high alpine habitat previously determined as Chlorella mirabilis. Molecular phylogeny of SSU rDNA (823 bp) showed that the two strains differed by one nucleotide only. Sequencing of the ITS2 region confirmed that both strains belong to the same species, but to distinct ribotypes. Therefore, the terrestrial strain was re-assessed as C. vulgaris. To study the response to environmental conditions experienced on land, we assessed the effects of irradiance and temperature on growth, of temperature on photosynthesis and respiration, and of desiccation and rehydration on photosynthetic performance. In contrast to the aquatic strain, the terrestrial strain tolerated higher temperatures and light conditions, had a higher photosynthesis-to-respiration ratio at 25°C, still grew at 30°C and was able to fully recover photosynthetic performance after desiccation at 84% relative humidity. The two strains differed most in their response to the dehydration/rehydration treatment, which was further investigated by untargeted GC-MS-based metabolite profiling to gain insights into metabolic traits differentiating the two strains. The two strains differed in their allocation of carbon and nitrogen into their primary metabolites. Overall, the terrestrial strain had higher contents of readily available nitrogen-based metabolites, especially amino acids and the polyamine putrescine. Dehydration and rehydration led to differential regulation of the amino acid metabolism, the tricarboxylic acid cycle and sucrose metabolism. The data are discussed with a view to differences in phenotypic plasticity of the two strains, and we suggest that the two genetically almost identical C. vulgaris strains are attractive models to study mechanisms that protect from abiotic stress factors, which are more frequent in terrestrial than aquatic habitats, such as desiccation and irradiation.

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Dataset Information

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats.

Publications

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats.

Similar Datasets

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