Increased agricultural activities driven by rising food demand have led to environmental problems mostly arising from the high levels of external inputs and resources that are required. Additionally, environmental changes, such as global warming, can lead to various biotic and abiotic stresses, which have negative impacts on crop production. Numerous solutions and agricultural strategies have been introduced to overcome these problems. One of the ways to improve plant production as well as to increase resistance towards biotic and abiotic stresses is by utilizing beneficial microbes as soil inoculants. A better understanding of the ability of Trichoderma to enhance crop production and the mechanisms that are involved are important for deriving maximum benefits from their exploitation. These versatile fungi hold great promise for the development of viable commercial products that can be used widely in agriculture for increasing crop productivity in a more sustainable way. Many previous reviews on Trichoderma have tended to focus on the mechanisms of Trichoderma in enhancing plant growth and yield. This current review discusses the sustainability aspect of using Trichoderma as plant growth regulators, the impact on plant growth and yield as well as their effects in regulating biotic and abiotic stresses.

Complete genome sequencing of cytoplasmically inherited chloroplast DNA provides novel insights into the origins of clonally propagated crops such as banana and plantain (Musa spp.). This study describes the structural organization of the chloroplast genome of M. balbisiana Colla and its phylogenetic relationship with other wild progenitors of the domesticated banana cultivars. The M. balbisiana chloroplast genome was sequenced using Illumina HiSeq 2000 platform, followed by a combination of de novo short-read assembly and reference-guided mapping of contigs to generate complete plastome sequence. The M. balbisiana chloroplast genome is 169,503 bp in length, exhibits a typical quadripartite structural organization with a large single-copy (LSC; 87,828 bp) region and a small single-copy (SSC; 11,547 bp) region interspersed between inverted repeat (IRa/b; 35,064 bp) regions. Overall, its gene content, size, and gene order were identical to that of M. acuminata Colla with extensive expansion of the inverted repeat-small single-copy (IR-SSC) junctions. Comparative analyses revealed the conserved IRa-SSC expansion in three wild Musa species and members of the order Zingiberales. In contrast, IRb-SSC expansion was conspicuously absent in the sister taxon M. textilis Nee and related species of Zingiberales. Interestingly, phylogenomic assessment based on whole-plastome and protein-coding gene sets have provided robust support for the association of M. balbisiana and M. textilis as a sister group, despite the variation in IRb-SSC expansion. Although the current study substantiates the infrageneric IRb-SSC fluctuations in Musaceae, extensive taxon sampling is necessary to confirm whether the accessions of section Musa have undergone independent IRb-SSC expansion relative to section Callimusa. Chloropl asts are a quintessential feature of land plants and algae, harboring oxygenic photosynthetic machinery and an array of metabolic pathways. Believed to have originated from endosymbiotic associations between cyanobacteria and eukaryotic cells, chloroplasts have evolved complex mechanisms of intracellular gene

BackgroundPanduratin A extracted from Boesenbergia rotunda is a flavonoid reported to possess a range of medicinal indications which include anti-dengue, anti-HIV, anti-cancer, antioxidant and anti-inflammatory properties. Boesenbergia rotunda is a plant from the Zingiberaceae family commonly used as a food ingredient and traditional medicine in Southeast Asia and China. Reports on the health benefits of secondary metabolites extracted from Boesenbergia rotunda over the last few years has resulted in rising demands for panduratin A. However large scale extraction has been hindered by the naturally low abundance of the compound and limited knowledge of its biosynthetic pathway.ResultsTranscriptome sequencing and digital gene expression (DGE) analysis of native and phenylalanine treated Boesenbergia rotunda cell suspension cultures were carried out to elucidate the key genes differentially expressed in the panduratin A biosynthetic pathway. Based on experiments that show increase in panduratin A production after 14 days post treatment with exogenous phenylalanine, an aromatic amino acid derived from the shikimic acid pathway, total RNA of untreated and 14 days post-phenylalanine treated cell suspension cultures were extracted and sequenced using next generation sequencing technology employing an Illumina-Solexa platform. The transcriptome data generated 101, 043 unigenes with 50, 932 (50.41%) successfully annotated in the public protein databases; including 49.93% (50, 447) in the non-redundant (NR) database, 34.63% (34, 989) in Swiss-Prot, 24,07% (24, 316) in Kyoto Encyclopedia of Genes and Genomes (KEGG) and 16.26% (16, 426) in Clusters of Orthologous Groups (COG). Through DGE analysis, we found that 14, 644 unigenes were up-regulated and 14, 379 unigenes down-regulated in response to exogenous phenylalanine treatment. In the phenylpropanoid pathway leading to the proposed panduratin A production, 2 up-regulated phenylalanine ammonia-lyase (PAL), 3 up-regulated 4-coumaroyl:coenzyme A ligase (4CL) and 1 up-regulated chalcone synthase (CHS) were found.ConclusionsThis is the first report of Boesenbergia rotunda de novo transcriptome data that could serve as a reference for gene or enzyme functional studies in the Zingiberaceae family. Although enzymes that are directly involved in the panduratin A biosynthetic pathway were not completely elucidated, the data provides an overall picture of gene regulation patterns leading to panduratin A production.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-984) contains supplementary material, which is available to authorized users.

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