[1] BUDDLE B M, DENIS M, ATTWOOD G T, et al.Strategies to reduce methane emissions from farmed ruminants grazing on pasture[J].The Veterinary Journal, 2011, 188(1):11-17.
[2] 秦楠, 栗东芳, 杨瑞馥.高通量测序技术及其在微生物学研究中的应用[J].微生物学报, 2011, 51(4):445-457.
[3] NAGALAKSHMI U, WANG Z, WAERN K, et al.The transcriptional landscape of the yeast genome defined by RNA sequencing[J].Science, 2008, 320(5881):1344-1349.
[4] WILHELM B T, MARGUERAT S, WATT S, et al.Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution[J].Nature, 2008, 453(7199):1239-1243.
[5] CARVALHAIS L C, DENNIS P G, TYSON G W, et al.Application of metatranscriptomics to soil environments[J].Journal of Microbiological Methods, 2012, 91(2):246-251.
[6] LU T T, LU G J, FAN D L, et al.Function annotation of rice transcriptome at single nucleotide resolution by RNA-Seq[J].Genome Research, 2010, 20(9):1238-1249.
[7] DAVID L A, MAURICE C F, CARMODY R N, et al.Diet rapidly and reproducibly alters the human gut microbiome[J].Nature, 2013, 505(7484):559-563.
[8] ROSENTHAL A Z, MATSON E G, ELDAR A, et al.RNA-Seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture[J].The ISME Journal, 2011, 5(7):1133-1142.
[9] BOMAR L, GRAF J.Investigation into the physiologies of Aeromonas veronii
in vitro and inside the digestive tract of the medicinal leech using RNA-Seq[J].Biological Bulletin, 2012, 223(1):155-166.
[10] BISANZ J E, MACKLAIM J M, GLOOR G B, et al.Bacterial metatranscriptome analysis of a probiotic yogurt using an RNA-Seq approach[J].International Dairy Journal, 2014, 39(2):284-292.
[11] BAKER B J, SHEIK C S, TAYLOR C A, et al.Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling[J].The ISME Journal, 2013, 7(10):1962-1973.
[12] MARDIS E R.Next-generation DNA sequencing methods[J].Annual Review of Genomics and Human Genetics, 2008, 9(1):387-402.
[13] GLENN T C.Field guide to next-generation DNA sequencers[J].Molecular Ecology Resources, 2011, 11(5):759-769.
[14] 沈圣, 屈彦纯, 张军.下一代测序技术在表观遗传学研究中的重要应用及进展[J].遗传, 2014, 36(3):256-275.
[15] WALL P K, LEEBENS-MACK J, CHANDERBALI A S, et al.Comparison of next generation sequencing technologies for transcriptome characterization[J].BMC Genomics, 2009, 10(1):347.
[16] CRAWFORD J E, GUELBEOGO W M, SANOU A, et al.
De novo transcriptome sequencing in
Anopheles funestus using Illumina RNA-Seq technology[J].PLoS One, 2010, 5(12):e14202.
[17] COCK P J A, FIELDS C J, GOTO N, et al.The sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants[J].Nucleic Acids Research, 2010, 38(6):1767-1771.
[18] 高山, 欧剑虹, 肖凯.R语言与Bioconductor生物信息学应用[M].天津:天津科技翻译出版有限公司, 2014:173-184.
[19] MORGAN M, ANDERS S, LAWRENCE M, et al.ShortRead:a bioconductor package for input, quality assessment and exploration of high-throughput sequence data[J].Bioinformatics, 2009, 25(19):2607-2608.
[20] RAMIREZ-GONZALEZ R H, LEGGETT R M, WAITE D, et al.StatsDB:platform-agnostic storage and understanding of next generation sequencing run metrics[J].F1000Research, 2013, 2:248.
[21] LOHSE M, BOLGER A M, NAGEL A, et al.RobiNA:a user-friendly, integrated software solution for RNA-Seq-based transcriptomics[J].Nucleic Acids Research, 2012, 40:W622-W627.
[22] WANG L, WANG S, LI W.RSeQC:quality control of RNA-Seq experiments[J].Bioinformatics, 2012, 28(16):2184-2185.
[23] TRAPNELL C, WILLIAMS B A, PERTEA G, et al.Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J].Nature Biotechnology, 2010, 28(5):511-515.
[24] VIJAY N, POELSTRA J W, KVNSTNER A, et al.Challenges and strategies in transcriptome assembly and differential gene expression quantification.A comprehensive
in silico assessment of RNA-Seq experiments[J].Molecular Ecology, 2013, 22(3):620-634.
[25] CARDENAS E, TIEDJE J M.New tools for discovering and characterizing microbial diversity[J].Current Opinion in Biotechnology, 2008, 19(6):544-549.
[26] 岳桂东, 高强, 罗龙海, 等.高通量测序技术在动植物研究领域中的应用[J].中国科学:生命科学, 2012, 42(2):107-124.
[27] DAI X, TIAN Y, LI J T, et al.Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen[J].Applied and Environmental Microbiology, 2015, 81(4):1375-1386.
[28] DODD D, MOON Y H, SWAMINATHAN K, et al.Transcriptomic analyses of xylan degradation by
Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes[J].The Journal of Biological Chemistry, 2010, 285(39):30261-30273.
[29] WANG T Y, CHEN H L, LU M Y, et al.Functional characterization of cellulases identified from the cow rumen fungus
Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses[J].Biotechnology for Biofuels, 2011, 4:24.
[30] LAWLEY B, SIMS I M, TANNOCK G W.Whole-transcriptome shotgun sequencing (RNA-Seq) screen reveals upregulation of cellobiose and motility operons of
Lactobacillus ruminis L5 during growth on tetrasaccharides derived from barley β-glucan[J].Applied and Environmental Microbiology, 2013, 79(18):5661-5669.
[31] FOUTS D E, SZPAKOWSKI S, PURUSHE J, et al.Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen[J].PLoS One, 2012, 7(11):e48289.
[32] ZENED A, COMBES S, CAUQUIL L, et al.Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets[J].FEMS Microbiology Ecology, 2013, 83(2):504-514.
[33] HENDERSON C.The effects of fatty acids on pure cultures of rumen bacteria[J].The Journal of Agricultural Science, 1973, 81(1):107-112.
[34] FAVA F, GITAU R, GRIFFIN B A, et al.The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome 'at-risk' population[J].International Journal of Obesity, 2013, 37(2):216-223.
[35] LI F Y, SUN X, HENDERSON G, et al.Comparative analyses of the bovine rumen microbiota using RNA and targeted DNA-based sequencing approaches[C]//2014 ADSA-ASAS-CSAS Joint Annual Meeting.[s.n.]:ASAS, 2014.
[36] DASSA B, BOROVOK I, RUIMY-ISRAELI V, et al.Rumen cellulosomics:divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains[J].PLoS One, 2014, 9(7):e99221.
[37] QI M, WANG P, O'TOOLE N, et al.Snapshot of the eukaryotic gene expression in muskoxen rumen-a metatranscriptomic approach[J].PLoS One, 2011, 6(5):e20521.
[38] 李劲亭, 苏小运, 田彦, 等.瘤胃细菌GH48家族糖苷水解酶基因多样性[J].微生物学报, 2014, 54(1):53-61.
[39] OLSON D G, TRIPATHI S A, GIANNONE R J, et al.Deletion of the Cel48S cellulase from
Clostridium thermocellum[J].Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(41):17727-17732.
[40] SUKHARNIKOV L O, ALAHUHTA M, BRUNECKY R, et al.Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48[J].The Journal of Biological Chemistry, 2012, 287 (49):41068-41077.
[41] XU C G, HUANG R R, TENG L, et al.Structure and regulation of the cellulose degradome in
Clostridium cellulolyticum[J].Biotechnology for Biofuels, 2013, 6(1):73.
[42] SCHELLENBERG J J, VERBEKE T J, MCQUEEN P, et al.Enhanced whole genome sequence and annotation of
Clostridium stercorarium DSM8532T using RNA-Seq transcriptomics and high-throughput proteomics[J].BMC Genomics, 2014, 15:567.
[43] TARTAR A, WHEELER M M, ZHOU X G, et al.Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite
Reticulitermes flavipes[J].Biotechnology for Biofuels, 2009, 2(1):25.
[44] POROYKO V, WHITE J R, WANG M, et al.Gut microbial gene expression in mother-fed and formula-fed piglets[J].PLoS One, 2010, 5(8):e12459.
[45] BOOIJINK C C G M, BOEKHORST J, ZOETENDAL E G, et al.Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed[J].Applied and Environmental Microbiology, 2010, 76(16):5533-5540.
京公网安备 11010802041926号