Abstract:
Background:Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes. Results:We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar 'Alamo' using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development. Conclusions:This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.
journal_name
Biotechnol Biofuelsjournal_title
Biotechnology for biofuelsauthors
Yan H,Bombarely A,Xu B,Frazier TP,Wang C,Chen P,Chen J,Hasing T,Cui C,Zhang X,Zhao B,Huang Ldoi
10.1186/s13068-018-1202-0subject
Has Abstractpub_date
2018-07-24 00:00:00pages
208issn
1754-6834pii
1202journal_volume
11pub_type
杂志文章abstract:Background:We previously developed several strategies to engineer plants to produce cost-efficient biofuels from plant biomass. Engineered Arabidopsis plants with low xylan and lignin content showed normal growth and improved saccharification efficiency under standard growth conditions. However, it remains to be determ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1196-7
更新日期:2018-07-18 00:00:00
abstract::[This corrects the article DOI: 10.1186/s13068-018-1097-9.]. ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章,已发布勘误
doi:10.1186/s13068-018-1185-x
更新日期:2018-07-03 00:00:00
abstract:BACKGROUND:Termite lignocellulose digestion is achieved through a collaboration of host plus prokaryotic and eukaryotic symbionts. In the present work, we took a combined host and symbiont metatranscriptomic approach for investigating the digestive contributions of host and symbiont in the lower termite Reticulitermes ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-2-25
更新日期:2009-10-15 00:00:00
abstract:Background:Black soldier fly (BSF, Hermetia illucens L.) can efficiently degrade organic wastes and transform into a high fat containing insect biomass that could be used as feedstock for biodiesel production. Meanwhile, the molecular regulatory basis of fat accumulation by BSF is still unclear; it is necessary to iden...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1531-7
更新日期:2019-08-09 00:00:00
abstract:BACKGROUND:The 'attached cultivation' technique for microalgae production, combining the immobilized biofilm technology with proper light dilution strategies, has shown improved biomass production and photosynthetic efficiency over conventional open-pond suspended cultures. However, how light is transferred and distrib...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-015-0240-0
更新日期:2015-03-26 00:00:00
abstract:BACKGROUND:Nitrogen limitation can induce neutral lipid accumulation in microalgae, as well as inhibiting their growth. Therefore, to obtain cultures with both high biomass and high lipid contents, and explore the lipid accumulation mechanisms, we implemented nitrogen deprivation in a model diatom Phaeodactylum tricorn...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-6-67
更新日期:2013-05-04 00:00:00
abstract:Background:Cyanobacteria have shown promising potential for the production of various biofuels and chemical feedstocks. Synechococcus elongatus UTEX 2973 is a fast-growing strain with pronounced tolerance to high temperatures and illumination. Hence, this strain appears to be ideal for the development of photosynthetic...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1215-8
更新日期:2018-08-04 00:00:00
abstract:Background:Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as anaerobic gut fungi. These gut fungi express ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1292-8
更新日期:2018-10-27 00:00:00
abstract:BACKGROUND:Non-productive cellulase adsorption onto lignin has always been deemed to negatively affect the enzymatic hydrolysis of lignocellulosic feedstocks. Therefore, understanding enzyme-lignin interactions is essential for the development of enzyme mixtures, the processes of lignocellulose hydrolysis, and the gene...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-7-38
更新日期:2014-03-14 00:00:00
abstract:BACKGROUND:Microalgae are highly efficient cellular factories that capture CO2 and are also alternative feedstock for biofuel production. Carbohydrates, proteins, and lipids are major biochemical components in microalgae. Carbohydrates or starch in microalgae are possible substrates in yeast fermentation for biofuel pr...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-017-0753-9
更新日期:2017-03-24 00:00:00
abstract:BACKGROUND:Mass transfer plays an important role in determining the efficiency of the biofuel conversion. However, adverse effect of shear stress from traditional agitation inhibits the cell growth and production of biofuels. How to enhance the mass transfer with less adverse effect is considered as one of the importan...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-015-0409-6
更新日期:2015-12-23 00:00:00
abstract:BACKGROUND:Replacing the energy-intensive evaporation of stillage by anaerobic digestion is one way of decreasing the energy demand of the lignocellulosic biomass to the ethanol process. The biogas can be upgraded and sold as transportation fuel, injected directly into the gas grid or be incinerated on-site for combine...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-3-21
更新日期:2010-09-15 00:00:00
abstract:UNLABELLED: BACKGROUND:Acetoin and 2,3-butanediol are two important biorefinery platform chemicals. They are currently fermented below 40°C using mesophilic strains, but the processes often suffer from bacterial contamination. RESULTS:This work reports the isolation and identification of a novel aerobic Geobacillus s...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-5-88
更新日期:2012-12-06 00:00:00
abstract:Background:The extremely thermophilic bacterium Caldicellulosiruptor lactoaceticus can degrade and metabolize untreated lignocellulosic biomass containing xylan. The mechanism of the bacterium for degradation of insoluble xylan in untreated biomass has not been revealed. Results:In the present study, the only annotate...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1480-1
更新日期:2019-06-08 00:00:00
abstract:BACKGROUND:The model alga Chlamydomonas reinhardtii requires acetate as a co-substrate for optimal production of lipids, and the addition of acetate to culture media has practical and economic implications for algal biofuel production. Here we demonstrate the growth of C. reinhardtii on acetate provided by mutant strai...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-014-0154-2
更新日期:2014-10-18 00:00:00
abstract:BACKGROUND:D-2,3-butanediol has many industrial applications such as chiral reagents, solvents, anti-freeze agents, and low freezing point fuels. Traditional D-2,3-butanediol producing microorganisms, such as Klebsiella pneumonia and K. xoytoca, are pathogenic and not capable of producing D-2,3-butanediol at high optic...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-7-16
更新日期:2014-01-29 00:00:00
abstract:Background:Butyric acid is a platform chemical material, the production of which has been greatly stimulated by the diverse range of downstream applications in many industries. In particular, higher quality butyric acid used in food and medicine, is more dependent on microbiological production methods. Hence, the bio-o...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-020-01741-9
更新日期:2020-06-03 00:00:00
abstract:BACKGROUND:In general, biofuel production involves biomass pretreatment and enzymatic saccharification, followed by the subsequent sugar conversion to biofuel via fermentation. The crucial step in the production of biofuel from biomass is the enzymatic saccharification. Many of the commercial cellulase enzyme cocktails...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-016-0587-x
更新日期:2016-08-22 00:00:00
abstract:Background:Populus (poplar) tree species including hybrid varieties are considered as promising biomass feedstock for biofuels and biochemicals production due to their fast growing, short vegetative cycle, and widely distribution. In this work, poplar was pretreated with acetic acid (AC) to produce xylooligosaccharides...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1423-x
更新日期:2019-04-15 00:00:00
abstract:Background:In the enzymatic conversion of biomass, it becomes an important issue to efficiently and cost-effectively degrade cellulose into fermentable glucose. β-Glucosidase (Bgluc), an essential member of cellulases, plays a critical role in cellulosic biomass degradation. The difficulty in improving the stability of...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1497-5
更新日期:2019-06-24 00:00:00
abstract:Background:A consolidated bioprocessing (CBP), where lignocellulose is converted into the desired product(s) in a single fermentative step without the addition of expensive degradative enzymes, represents the ideal solution of renewable routes to chemicals and fuels. Members of the genus Geobacillus are able to grow at...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1540-6
更新日期:2019-08-20 00:00:00
abstract:BACKGROUND:Multidimensional solid-state nuclear magnetic resonance (ssNMR) spectroscopy has emerged as an indispensable technique for resolving polymer structure and intermolecular packing in primary and secondary plant cell walls. Isotope (13C) enrichment provides feasible sensitivity for measuring 2D/3D correlation s...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-020-01858-x
更新日期:2021-01-07 00:00:00
abstract:BACKGROUND:Solid-state anaerobic digestion (SS-AD) has been increasingly used for lignocellulosic biomass treatment. However, the separate reactor required for pretreatment prior digestion, poor treatment capacity, and process stability inhibit further development of the SS-AD. In this study, a novel method called SS-A...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-016-0530-1
更新日期:2016-06-01 00:00:00
abstract:Background:Amelioration of biofuel feedstock of microalgae using sustainable means through synthetic ecology is a promising strategy. The co-cultivation model (Tetraselmis striata and Pelagibaca bermudensis) was evaluated for the robust biofuel production under varying stressors as well as with the selected two-stage c...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1097-9
更新日期:2018-04-07 00:00:00
abstract:Background:Sustainable biofuels, which are widely considered as an attractive alternative to fossil fuels, can be generated by utilizing various biomass from the environment. Marine biomass, such as red algal biomass, is regarded as one potential renewable substrate source for biofuels conversion due to its abundance o...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1044-9
更新日期:2018-02-15 00:00:00
abstract:BACKGROUND:Cyanobacteria are an attractive candidate for the production of biofuel because of their ability to capture carbon dioxide by photosynthesis and grow on non-arable land. However, because huge quantities of water are required for cultivation, strict water management is one of the greatest issues in algae- and...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-7-56
更新日期:2014-04-09 00:00:00
abstract:Background:Beer is the most popular alcoholic beverage worldwide. In the manufacture of beer, various by-products and residues are generated, and the most abundant (85% of total by-products) are spent grains. Thanks to its high (hemi)cellulose content (about 50% w/w dry weight), this secondary raw material is attractiv...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1383-1
更新日期:2019-03-05 00:00:00
abstract:Background:The crystallinity of cellulose is a principal factor limiting the efficient hydrolysis of biomass to fermentable sugars or direct catalytic conversion to biofuel components. We evaluated the impact of TFA-induced gelatinization of crystalline cellulose on enhancement of enzymatic digestion and catalytic conv...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-017-0999-2
更新日期:2017-12-27 00:00:00
abstract:BACKGROUND:Microbial lipid production using renewable feedstock shows great promise for the biodiesel industry. RESULTS:In this study, the ability of a lipid-engineered Yarrowia lipolytica strain JMY4086 to produce lipids using molasses and crude glycerol under different oxygenation conditions and at different inoculu...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-015-0286-z
更新日期:2015-07-25 00:00:00
abstract:BACKGROUND:Hydrolysates of plant biomass used for the production of lignocellulosic biofuels typically contain sugar mixtures consisting mainly of D-glucose and D-xylose, and minor amounts of L-arabinose. The yeast Saccharomyces cerevisiae is the preferred microorganism for the fermentative production of ethanol but is...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-4-38
更新日期:2011-10-12 00:00:00