Dataset Information

Piptochaetium fuscum (Nees ex Steud.) Barkworth, Ciald., & Gandhi, a new combination replacing Piptochaetium setosum (Trin.) Arechav.

ABSTRACT: A new name, Piptochaetium fuscum, is provided for a taxon hitherto known as Piptochaetium setosum (Trin.) Arechav. Morphological, anatomical, and molecular studies that argue against including Piptochaetium in Stipa, and hence use of S. purpurata (Phil.) Columbus & J.P. Sm., are cited.

SUBMITTER: Barkworth ME

PROVIDER: S-EPMC4023335 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Piptochaetium fuscum (Nees ex Steud.) Barkworth, Ciald., & Gandhi, a new combination replacing Piptochaetium setosum (Trin.) Arechav.

Barkworth Mary E ME Cialdella Ana María AM Gandhi Kanchi K

PhytoKeys 20140226 35

A new name, Piptochaetium fuscum, is provided for a taxon hitherto known as Piptochaetium setosum (Trin.) Arechav. Morphological, anatomical, and molecular studies that argue against including Piptochaetium in Stipa, and hence use of S. purpurata (Phil.) Columbus & J.P. Sm., are cited. ...[more]

PMID: 24843286

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Project description:BackgroundSugarcane is an important sugar and energy crop that is widely planted in the world. Among the environmental stresses, the water-deficit stress is the most limiting to plant productivity. Some groups have used PCR-based and microarray technologies to investigate the gene expression changes of multiple sugarcane cultivars under water stress. Our knowledge about sugarcane genes in response to water deficit is still poor.ResultsA wild sugarcane type, Saccharum narenga, was selected and treated with drought stress for 22 days. Leaves from drought treated (DTS) and control (CK) plants were obtained for deep sequencing. Paired-end sequencing enabled us to assemble 104,644 genes (N50 = 1605 bp), of which 38,721 were aligned to other databases, such as UniProt, NR, GO, KEGG and Pfam. Single-end and paired-end sequencing identified 30,297 genes (> 5 TPM) in all samples. Compared to CK, 3389 differentially expressed genes (DEGs) were identified in DTS samples, comprising 1772 up-regulated and 1617 down-regulated genes. Functional analysis showed that the DEGs were involved in biological pathways like response to blue light, metabolic pathways and plant hormone signal transduction. We further observed the expression patterns of several important gene families, including aquaporins, late embryogenesis abundant proteins, auxin related proteins, transcription factors (TFs), heat shock proteins, light harvesting chlorophyll a-b binding proteins, disease resistance proteins, and ribosomal proteins. Interestingly, the regulation of genes varied among different subfamilies of aquaporin and ribosomal proteins. In addition, DIVARICATA and heat stress TFs were first reported in sugarcane leaves in response to water deficit. Further, we showed potential miRNAs that might be involved in the regulation of gene changes in sugarcane leaves under the water-deficit stress.ConclusionsThis is the first transcriptome study of Saccharum narenga and the assembled genes are a valuable resource for future research. Our findings will improve the understanding of the mechanism of gene regulation in sugarcane leaves under the water-deficit stress. The output of this study will also contribute to the sugarcane breeding program.

Project description:Auxin Response Factors (ARFs) make up a plant-specific transcription factor family that mainly couples perception of the phytohormone, auxin, and gene expression programs and plays an important and multi-faceted role during plant growth and development. Lemongrass (Cymbopogon flexuosus) is a representative Cymbopogon species widely used in gardening, beverages, fragrances, traditional medicine, and heavy metal phytoremediation. Biomass yield is an important trait for several agro-economic purposes of lemongrass, such as landscaping, essential oil production, and phytoremediation. Therefore, we performed gene mining of CfARFs and identified 26 and 27 CfARF-encoding genes in each of the haplotype genomes of lemongrass, respectively. Phylogenetic and domain architecture analyses showed that CfARFs can be divided into four groups, among which groups 1, 2, and 3 correspond to activator, repressor, and ETTN-like ARFs, respectively. To identify the CfARFs that may play major roles during the growth of lemongrass plants, RNA-seq was performed on three tissues (leaf, stem, and root) and four developmental stages (3-leaf, 4-leaf, 5-leaf. and mature stages). The expression profiling of CfARFs identified several highly expressed activator and repressor CfARFs and three CfARFs (CfARF3, 18, and 35) with gradually increased levels during leaf growth. Haplotype-resolved transcriptome analysis revealed that biallelic expression dominance is frequent among CfARFs and contributes to their gene expression patterns. In addition, co-expression network analysis identified the modules enriched with CfARFs. By establishing orthologous relationships among CfARFs, sorghum ARFs, and maize ARFs, we showed that CfARFs were mainly expanded by whole-genome duplications, and that the duplicated CfARFs might have been divergent due to differential expression and variations in domains and motifs. Our work provides a detailed catalog of CfARFs in lemongrass, representing a first step toward characterizing CfARF functions, and may be useful in molecular breeding to enhance lemongrass plant growth.

Dataset Information

Piptochaetium fuscum (Nees ex Steud.) Barkworth, Ciald., & Gandhi, a new combination replacing Piptochaetium setosum (Trin.) Arechav.

Publications

Piptochaetium fuscum (Nees ex Steud.) Barkworth, Ciald., & Gandhi, a new combination replacing Piptochaetium setosum (Trin.) Arechav.

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