Transcriptome profiling of cold acclimation in bermudagrass (Cynodon dactylon)

Zhu, Huisen; Yu, Xiuju; Xu, Tao; Wang, Tailiang; Du, Liangcheng; Ren, Guoqing; Kuan-hu, Dong

doi:10.1016/j.scienta.2015.08.024

Cited by 17 publications

(10 citation statements)

References 32 publications

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“…Protoplast transformation may be another choice under the precondition of the implementation of the protoplast regeneration. With the great progress in next-generation sequencing, large amounts of transcriptomics and proteomics statistical data related to bermudagrass resistance to low temperature [8,9,52], drought [83,84] and salt stress [85][86][87], have been published. We can take full advantage of these data for studying the molecular mechanism of bermudagrass resistance and resistance breeding.…”

Section: Prospectsmentioning

confidence: 99%

“…Due to the importance of bermudagrass, molecular techniques involving amplified fragment length polymorphism (AFLP), inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD), sequence related amplified polymorphism (SRAP) and simple sequence repeats (SSRs) have long been applied in improving bermudagrass, with a focus on enhancing its stress resistance and analysing its germplasm and genetic diversity for constructing linkage maps. Recently, RNA-Seq have been used for analysing the molecular basis of the physiological processes [8,9]. These studies have provided insights into the differences between species or varieties and the reasons of their stress tolerance, which may help accelerate the genetic improvement of bermudagrass.…”

Section: Introductionmentioning

confidence: 99%

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Genetic resources and genetic transformation in bermudagrass – a review

Huang

Wang

Liang

2017

Biotechnology & Biotechnological Equipment

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Bermudagrass is widely distributed as a warm-season turf and forage grass in the temperate and tropical zones around the world. Its strong vegetative reproduction and ability to withstand drought make it an ideal species as a most used warm-season forage grass and turfgrass. Genetic transformation is an important tool for the study of gene function and for germplasm improvement in bermudagrass. This paper attempts to present a recent review on genetic resources, plant regeneration and genetic transformation in bermudagrass. We first review the various genetic resources and collection of bermudagrass. Then the explants, basal medium and the effect of different cultivars and plant growth regulators on plant regeneration in bermudagrass are also summarized. Last, we outline the main areas of progress in genetic transformation with either the biolistic or Agrobacterium-mediated method in bermudagrass, and discuss various factors that influence Agrobacterium-mediated transformation. However, the question that still remains is why there have been no genetic modification reports on bermudagrass for 10 years.

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Section: Prospectsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic resources and genetic transformation in bermudagrass – a review

Huang

Wang

Liang

2017

Biotechnology & Biotechnological Equipment

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“…Transcriptome analysis could identify the type and number of intracellular key genes and reveal the metabolic pathways at a molecular level [ 24 , 25 ]. At present, several technologies have been applied for transcriptome sequencing.…”

Section: Introductionmentioning

confidence: 99%

Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng

Liu

Wang

et al. 2020

IJMS

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Pseudotaxus chienii, a rare tertiary relict species with economic and ecological value, is a representative of the monotypic genus Pseudotaxus that is endemic to China. P. chienii can adapt well to habitat isolation and ecological heterogeneity under a variety of climate and soil conditions, and is able to survive in harsh environments. However, little is known about the molecular and genetic resources of this long-lived conifer. Herein, we sequenced the transcriptomes of four organs of P. chienii using the PacBio Isoform Sequencing and Illumina RNA Sequencing platforms. Based on the PacBio Iso-Seq data, we obtained 44,896, 58,082, 50,485, and 67,638 full-length unigenes from the root, stem, leaf, and strobilus, respectively, with a mean length of 2692 bp, and a mean N50 length of 3010.75 bp. We then comprehensively annotated these unigenes. The number of organ-specific expressed unigenes ranged from 4393 in leaf to 9124 in strobilus, suggesting their special roles in physiological processes, organ development, and adaptability in the different four organs. A total of 16,562 differentially expressed genes (DEGs) were identified among the four organs and clustered into six subclusters. The gene families related to biotic/abiotic factors, including the TPS, CYP450, and HSP families, were characterized. The expression levels of most DEGs in the phenylpropanoid biosynthesis pathway and plant–pathogen interactions were higher in the root than in the three other organs, suggesting that root constitutes the main organ of defensive compound synthesis and accumulation and has a stronger ability to respond to stress. The sequences were analyzed to predict transcription factors, long non-coding RNAs, and alternative splicing events. The expression levels of most DEGs of C2H2, C3H, bHLH, and bZIP families in the root and stem were higher than those in the leaf and strobilus, indicating that these TFs may play a crucial role in the survival of the root and stem. These results comprise the first comprehensive gene expression profiles obtained for different organs of P. chienii. Our findings will facilitate further studies on the functional genomics, adaptive evolution, and phylogeny of P. chienii, and lay the foundation for the development of conservation strategies for this endangered conifer.

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“…Transcriptomics, dealing with the transcribed regions throughout the genome for various functions of our interest underlying a corresponding biological process, is a sensitive, effective and reliable method to explore the gene expressions (Marioni et al, 2008;Haas & Zody, 2010;Wu et al, 2015;Zhu et al, 2015). RNA-sequencing is a high-throughput screening technology that could be used to isolate and screen the genes which were differentially expressed under specific biological processes and unveil the functional elements in the genome and interpret the phenotypic variation associated with the gene expressions (Garber et al, 2011;Wu et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Metabolic pathways analysis and identification of heat response genes of pineapple [Ananas comosus (L.) Merr.] fruit affected by elevated postharvest temperature

Liu¹,

Liu²,

ShiZi³

et al. 2019

PAK.J.BOT.

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Pineapple [Ananas comosus (L.) Merr.] is an important tropical fruit. The pineapple fruits that are ripened in the hightemperature season have better quality, whereas those ripened in low-temperature season are acidic in taste. Elevated postharvest temperature (EPT) could enhance the quality of winter-harvested pineapple fruit. Based on transcriptome and differentially expressed genes analysis, we explored the GO (Gene Ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathways associated with the EPT treatment and the differentially expressed heat response genes of pineapple fruit after EPT treatment. GO classifications suggested that DEGs (differentially expressed genes) were predominantly annotated to "response to stimulus", "response to external stimulus" and "aromatic compound biosynthetic process" in the biological process ontology, "hydrolase activity" and "glucosidase activity" in the molecular function ontology, as well as "intrinsic to membrane" and "cell wall" in the cellular component ontology. KEGG metabolic pathways analysis revealed that the DEGs were dominantly enriched to "starch and sucrose metabolism", "biosynthesis of secondary metabolites", "pentose and glucuronate interconversions", "carotenoid biosynthesis", "metabolic pathways" "galactose metabolism" and "plant hormone signal transduction". Nineteen HSP (heat shock protein) and sHSP (small HSP) DEGs were screened, and most of them were up-regulated by EPT. Most of the transcription factor genes, including HSF, bHLH, WRKY, MYB, AP2/ERF, bZIP and NAC, were down-regulated by EPT. The SOD (Superoxide dismutase) genes were induced by EPT, while most of the POD (Peroxidase) and CAT (Catalase) genes were repressed. This work would help to understand the molecular mechanisms for EPT process to improve the quality of pineapple fruits.

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Transcriptome profiling of cold acclimation in bermudagrass (Cynodon dactylon)

Cited by 17 publications

References 32 publications

Genetic resources and genetic transformation in bermudagrass – a review

Genetic resources and genetic transformation in bermudagrass – a review

Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng

Metabolic pathways analysis and identification of heat response genes of pineapple [Ananas comosus (L.) Merr.] fruit affected by elevated postharvest temperature

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