RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L.
High-throughput transcriptome provides an unbiased approach for understanding the genetic basis and gene functions in response to different conditions. Here we sequenced RNA-seq libraries derived from a Bombax ceiba L. system under a controlled experiment. As a known medicinal and ornamental plant,...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2015-01-01
|
| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.4137/EBO.S20620 |
| _version_ | 1819050409107390464 |
|---|---|
| author | Zhili Zhou Huancheng Ma Kevin Lin Youjie Zhao Yuan Chen Zhi Xiong Liuyang Wang Bin Tian |
| author_facet | Zhili Zhou Huancheng Ma Kevin Lin Youjie Zhao Yuan Chen Zhi Xiong Liuyang Wang Bin Tian |
| author_sort | Zhili Zhou |
| collection | DOAJ |
| description | High-throughput transcriptome provides an unbiased approach for understanding the genetic basis and gene functions in response to different conditions. Here we sequenced RNA-seq libraries derived from a Bombax ceiba L. system under a controlled experiment. As a known medicinal and ornamental plant, B. ceiba grows mainly in hot-dry monsoon rainforests in Southeast Asia and Australia. Due to the specific growth environment, it has evolved a unique system that enables a physiologic response to drought stress. To date, few studies have characterized the genome-wide features of drought endurance in B. ceiba. In this study, we first attempted to characterize and identify the most differentially expressed genes and associated functional pathways under drought treatment and normal condition. Using RNA-seq technology, we generated the first transcriptome of B. ceiba and identified 59 differentially expressed genes with greater than 1,000-fold changes under two conditions. The set of upregulated genes implicates interplay among various pathways: plants growth, ubiquitin-mediated proteolysis, polysaccharides hydrolyzation, oxidative phosphorylation and photosynthesis, etc. In contrast, genes associated with stem growth, cell division, fruit ripening senescence, disease resistance, and proline synthesis are repressed. Notably, key genes of high RPKM levels in drought are AUX1, JAZ , and psbS , which are known to regulate the growth of plants, the resistance against abiotic stress, and the photosynthesis process. Furthermore, 16,656 microsatellite markers and 3,071 single-nucleotide polymorphisms (SNPs) were predicted by in silico methods. The identification and functional annotation of differentially expressed genes, microsatellites, and SNPs represent a major step forward and would serve as a valuable resource for understanding the complexity underlying drought endurance and adaptation in B. ceiba . |
| first_indexed | 2024-12-21T11:47:35Z |
| format | Article |
| id | doaj.art-5427762a891e449a8d00c74a2c6d2840 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-21T11:47:35Z |
| publishDate | 2015-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-5427762a891e449a8d00c74a2c6d28402022-12-21T19:05:08ZengSAGE PublishingEvolutionary Bioinformatics1176-93432015-01-0111s110.4137/EBO.S20620RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L.Zhili Zhou0Huancheng Ma1Kevin Lin2Youjie Zhao3Yuan Chen4Zhi Xiong5Liuyang Wang6Bin Tian7Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, China.Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China.Department of Molecular Genetics and Microbiology.Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China.Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, USA.Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China.Department of Molecular Genetics and Microbiology.Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, China.High-throughput transcriptome provides an unbiased approach for understanding the genetic basis and gene functions in response to different conditions. Here we sequenced RNA-seq libraries derived from a Bombax ceiba L. system under a controlled experiment. As a known medicinal and ornamental plant, B. ceiba grows mainly in hot-dry monsoon rainforests in Southeast Asia and Australia. Due to the specific growth environment, it has evolved a unique system that enables a physiologic response to drought stress. To date, few studies have characterized the genome-wide features of drought endurance in B. ceiba. In this study, we first attempted to characterize and identify the most differentially expressed genes and associated functional pathways under drought treatment and normal condition. Using RNA-seq technology, we generated the first transcriptome of B. ceiba and identified 59 differentially expressed genes with greater than 1,000-fold changes under two conditions. The set of upregulated genes implicates interplay among various pathways: plants growth, ubiquitin-mediated proteolysis, polysaccharides hydrolyzation, oxidative phosphorylation and photosynthesis, etc. In contrast, genes associated with stem growth, cell division, fruit ripening senescence, disease resistance, and proline synthesis are repressed. Notably, key genes of high RPKM levels in drought are AUX1, JAZ , and psbS , which are known to regulate the growth of plants, the resistance against abiotic stress, and the photosynthesis process. Furthermore, 16,656 microsatellite markers and 3,071 single-nucleotide polymorphisms (SNPs) were predicted by in silico methods. The identification and functional annotation of differentially expressed genes, microsatellites, and SNPs represent a major step forward and would serve as a valuable resource for understanding the complexity underlying drought endurance and adaptation in B. ceiba .https://doi.org/10.4137/EBO.S20620 |
| spellingShingle | Zhili Zhou Huancheng Ma Kevin Lin Youjie Zhao Yuan Chen Zhi Xiong Liuyang Wang Bin Tian RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L. Evolutionary Bioinformatics |
| title | RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L. |
| title_full | RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L. |
| title_fullStr | RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L. |
| title_full_unstemmed | RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L. |
| title_short | RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, L. |
| title_sort | rna seq reveals complicated transcriptomic responses to drought stress in a nonmodel tropic plant l |
| url | https://doi.org/10.4137/EBO.S20620 |
| work_keys_str_mv | AT zhilizhou rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl AT huanchengma rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl AT kevinlin rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl AT youjiezhao rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl AT yuanchen rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl AT zhixiong rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl AT liuyangwang rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl AT bintian rnaseqrevealscomplicatedtranscriptomicresponsestodroughtstressinanonmodeltropicplantl |