Isothermal Strand-Displacement Amplification Applications for High-Throughput Genomics

Detter, John C.; Jett, Jamie; Lucas, Susan; Dalin, Eileen; Arellano, André R.; Wang, Mei; Nelson, John; Chapman, Jarrod; Lou, Yunian; Rokhsar, Daniel S.; Hawkins, Trevor; Richardson, Paul M.

doi:10.1006/geno.2002.7020

Cited by 84 publications

(63 citation statements)

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“…The genome of T. reesei was shotgun sequenced 6 to approximately ninefold coverage from three libraries (insert sizes of 3 kb, 8 kb and 40 kb) totaling 433,863 reads (Supplementary Table 1 online). These data, in addition to more than 6,000 BAC-end sequences 7 , yielded a high-quality draft assembly using the Department of Energy Joint Genome Institute (JGI) shotgun assembler Jazz 8 .…”

Section: Features Of the T Reesei Genomementioning

confidence: 99%

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

et al. 2008

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Section: Features Of the T Reesei Genomementioning

confidence: 99%

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

et al. 2008

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“…The 25 temperature optima for these xylanases range from 45 °C to 70 °C ( Table 2). These results 26 suggest that M. thermophila and T. terrestris not only possess diverse enzyme activities for 27 degradation of plant cell wall polysaccharides, they have also evolved diverse properties for 28 these enzymes that enable efficient hydrolysis over a range of temperatures. The diversity of 29 enzyme activities and properties may help to explain the ubiquity of these organisms in 1 decomposing biomass.…”

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confidence: 90%

“…1). The largest gene families in the genomes of M. thermophila 26 and T. terrestris include transporters (e.g., MFS, ABC, AAA and sugar transporters) and proteins 27 involved in signaling (e.g., protein kinases and WD40) as shown in Supplementary Table 2, 28 often with more genes of each type in T. terrestris. Several Pfam domains appear to be expanded 29 in the Chaetomiaceae, including glycoside hydrolase families GH61 and GH11, and hypothetical 1 proteins with a DUF1996 domain of unknown function (Supplementary Table 3).…”

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“…Recently, it was reported that certain GH61 proteins lack measurable hydrolytic 25 activity by themselves, but in the presence of various divalent metal ions, they can substantially 26 enhance lignocellulosic biomass hydrolysis by cellulases and reduce the amount of cellulase 27 required for hydrolysis of biomass polysaccharides 10 . The expansion of GH61 genes in this 28 group of fungi may have evolved as a modified strategy for deconstruction of biomass 29 polysaccharides compared to that of other species such as T. reesei. is suggested by the .…”

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“…Distinguishing thermophilic from mesophilic fungi 28 Compared to the closely related mesophile C. globosum, the genomes of M. thermophila and T. 29 terrestris contain larger fractions of repetitive sequences that have low GC content, introducing 30 significant GC variation (Supplementary Fig. 8).…”

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Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

et al. 2011

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Thermostable enzymes and thermophilic cell factories may afford economic advantages inFurthermore, we present evidence suggesting that aside from representing a potential 9 reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using 10 classical and molecular genetics. 11Rapid, efficient and robust enzymatic degradation of biomass-derived polysaccharides is 12 currently a major challenge for biofuel production. A prerequisite is the availability of enzymes 13 that hydrolyze cellulose, hemicellulose and other polysaccharides into fermentable sugars at 14 conditions suitable for industrial use. The best studied and most widely used cellulases and to overcome these obstacles is to raise the reaction temperature, thereby increasing hydrolytic 20 rates and reducing contamination risks. AT-rich repetitive regions (Fig. 1) To examine the strategy used by these thermophiles for decomposition of plant cell wall 9 polysaccharides, we used RNA-Seq to compare transcript profiles during growth on barley straw 10 or alfalfa straw to growth on glucose. Alfalfa was chosen to represent dicotyledonous plants, 11 whereas barley was used to represent monocotyledon plants. The major difference between these 12 materials is that the carbohydrates from barley cell wall are mainly cellulose and hemicellulose 13 with a negligible amount of pectin 11 , whereas alfalfa cell wall contains pectin and xylan in 14 roughly similar proportions, each consisting of 15-20% of total carbohydrates 12, . 15 We observed notable differences between the transcriptional profiles of genes encoding conditions. For example, the orthologs in Clades A, B, E, G and P of GH61 are upregulated 8 under growth in complex substrates for both thermophiles (Fig. 2b). An even more striking 9 correlation between transcript levels and orthologs is evident for the GH6 and GH7 cellulases 10 ( Supplementary Fig. 7) where the transcript profiles for the orthologs of the two organisms are Table 7). Thermophilic fungi are major components of the microflora in self-heating composts. They 9 break down cellulose at a faster rate than prodigious, mesophilic cellulase producers such as T. Tables 11-14). On the basis of 24 our comparative analyses of the genomes from two thermophilic fungi, we conclude that their 25 nucleotide and protein features are different from those observed in thermophilic prokaryotes. 26 We also investigated the possibility that thermophilic fungi possess major differences in 27 processes mediating thermophily including heat shock, oxidative stress, membrane biosynthesis, 28 chromatin structure and modification, and fungal cell wall metabolism. We compared the 29 proteins predicted to be involved in these processes in C. globosum, M. thermophila and T. 30 terrestris, but were unable to find differences that can convincingly be interpreted as the Fig. 9). Within the Sordiariales, thermophily 6 is restricted to subgroups of the family Chaetomiaceae. Among fungi more broadly, thermophily 7 also exists in the Zygomycota, but it ...

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Methods in Viral Metagenomics

Thurber

2011

Handbook of Molecular Microbial Ecology II

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Isothermal Strand-Displacement Amplification Applications for High-Throughput Genomics

Abstract: Rolling circle replication is typically employed by certain viruses to replicate their circular genomes in nature 3 . Rolling circle amplification (RCA) has traditionally been used in the laboratory using specific primer sequences to replicate circular sequences for

Cited by 84 publications

References 13 publications

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Methods in Viral Metagenomics

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