Transcriptome Sequencing on Fruiting Body of Agaricus bisporus in Developing Stages
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摘要: 对双孢蘑菇As2796子实体发育4个不同阶段样品的转录组进行测序，并与双孢蘑菇参考基因组进行序列比对。共比对到9 207个转录本，发掘新基因393个，其中164个得到功能注释。基于比对结果进行各基因在不同样品中的表达量分析，识别差异表达基因，发现原基期与其他3个不同发育时期有316个共同差异基因。对差异基因进行功能注释和富集分析，可为进一步研究双孢蘑菇子实体生长发育的相关基因奠定基础。Abstract: Samples of Agaricus bisporus As2796 fruiting bodies in 4 developmental stages were collected for transcriptome sequencing. After aligned with the reference genome sequence of the mushroom, 9 207 transcripts were identified. Among them, 393 were new genes with 164 being functionally annotated. The expression level of the genes was analyzed to differentiate the samples. The alignments showed an overlapping of 316 differentially expressed genes between the primordium and the 3 other developmental stages. An analysis and function evaluation on these genes were performed for further study on the growth and development of A. bisporus fruiting body.
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Key words:
- Agaricus bisporus /
- fruiting body development /
- transcriptome sequencing
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图 1 双孢蘑菇As2796子实体不同发育阶段与原基期相比的差异表达基因数目韦恩图
Figure 1. Venn diagram on number of differentially expressed genes of A. bisporus As2796 fruiting bodies at primordium and other developmental stages
图 2 双孢蘑菇As2796子实体幼菇期与原基期差异表达基因的COG分类
Figure 2. COG annotation of differentially expressed genes between young and primordium stages of A. bisporus As2796 fruiting bodies
图 3 双孢蘑菇As2796子实体开伞期与原基期相比差异基因KEGG通路类型
Figure 3. KEGG pathway types of differentially expressed genes between opening and primordium stages of A. bisporus As2796 fruiting bodies
表 1 样品测序数据及与所选参考基因组的序列比对结果
Table 1. Statistical sequencing data and alignment of samples with reference genome
样品 编号 所有Reads 比对上的Reads
(占比/%)GC含量
/%≥Q30比例
/%As2796原基期 T01 35, 666, 572 26, 745, 594 (74.99) 49.06 87.10 As2796幼菇期 T02 35, 313, 022 27, 062, 540 (76.64) 49.39 86.34 As2796采收期 T03 38, 280, 048 29, 421, 017 (76.86) 49.27 86.59 As2796开伞期 T04 38, 250, 636 28, 047, 724 (73.33) 49.55 86.57 
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表 2 双孢蘑菇As2796子实体不同发育阶段新基因功能注释结果
Table 2. Statistics on annotated new genes of A. bisporus As2796 fruiting bodies at different developmental stages
用于注释的数据库 获注释的新基因数目 COG 10 GO 11 KEGG 15 Swiss-Prot 15 nr 164 All 164
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表 3 双孢蘑菇As2796子实体不同发育阶段与原基期相比的差异表达基因数目统计
Table 3. Number of differentially expressed genes of A. bisporus As2796 fruiting bodies at primordium and other developmental stages
差异表达基因集 所有DEG 上调表达DEG 下调表达DEG T01_vs_T02 703 199 504 T01_vs_T03 891 266 625 T01_vs_T04 953 433 520
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表 4 双孢蘑菇As2796子实体不同发育阶段与原基期相比连续上下调差异表达部分基因
Table 4. Part of differentially expressed genes up-or down-regulated continuously of A. bisporus As2796 fruiting bodies at primordium and other developmental stages
编号 基因ID 相对表达量FPKM 基因长度/bp 基因注释 T01 T02 T03 T04 1 estExt_fgenesh2_pg.C_140114 0.00 4.27 5.60 13.66 1070 hypothetical protein AGABI2DRAFT_181292 2 estExt_Genewise1.C_120616 0.12 1.39 8.59 28.39 761 Uncharacterized hemerythrin-like protein C869.06c 3 estExt_fgenesh2_pg.C_70433 0.12 0.16 0.55 5.85 2232 hypothetical protein AGABI2DRAFT_179499 4 e_gw1.3.1046.1 0.14 0.44 0.95 3.13 1326 hypothetical protein AGABI2DRAFT_65418 5 fgenesh2_kg.4_668_2_898_CFAF_CFAG_CFAH_EXTA 0.20 2.96 6.50 8.17 603 Cell wall/membrane/envelope biogenesis 6 estExt_fgenesh2_kg.C_10169 24.02 15.49 6.72 0.00 925 Translation, ribosomal structure and biogenesis 7 Agaricus_newGene_232 15.09 4.80 0.77 0.00 510 hypothetical protein AGABI1DRAFT_132181 8 Agaricus_newGene_387 10.56 6.96 0.68 0.00 460 Null 9 Agaricus_newGene_471 15.32 0.61 0.11 0.00 883 Null 10 estExt_fgenesh2_kg.C_70465 2.33 1.93 0.76 0.00 1908 hypothetical protein AGABI2DRAFT_193962 11 fgenesh2_kg.9_95_2_1845_CFAF_CFAG_CFAH_EXTA 9.85 3.61 0.00 0.00 665 Hydrophobin-3 (Precursor) 12 fgenesh2_pm.14_33 25.79 5.37 1.72 0.00 447 hypothetical protein AGABI2DRAFT_154209
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表 5 注释的差异表达基因数量统计
Table 5. Statistics of annotated differentially expressed genes
差异表达基因集 差异表达基因总数 各数据库注释到的差异表达基因数 COG GO KEGG NR Swiss-Prot T01_vs_T02 676 289 242 156 676 351 T01_vs_T03 862 352 306 194 862 435 T01_vs_T04 928 393 364 265 928 490
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[1] 王泽生, 廖剑华, 陈美元, 等.双孢蘑菇遗传育种和产业发展[J].食用菌学报, 2012, 19(3):1-14. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=syjxb201203001 [2] SONNENBERG A S M, BAARS J J P, GAO W, et al. Developments in breeding of Agaricus bisporus var. bisporus: progress made and technical and legal hurdles to take[J]. Applied Microbiology and Biotechnology, 2017, 101(5): 1819-1829. http://cn.bing.com/academic/profile?id=d41b0fdc09bc9f423a692b53cb345927&encoded=0&v=paper_preview&mkt=zh-cn [3] 陈美元, 廖剑华, 李洪荣, 等. 20个双孢蘑菇核心种质的重测序初步分析[C]//中国菌物学会年会论文集. 2015: 59-67. [4] 陈美元, 廖剑华, 李洪荣, 等.双孢蘑菇子实体发育差异蛋白质组分析[J].菌物学报, 2015, 34(6):1153-1164. http://mall.cnki.net/magazine/Article/JWXT201305011.htm [5] KIM D, PERTEA G, TRAPNELL C, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions[J]. Genome Biology, 2013, 14:R36. doi: 10.1186/gb-2013-14-4-r36 [6] FLOREA L, SONG L, SALZBERG S L. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues[J]. F1000 Research, 2013, 2:188. http://cn.bing.com/academic/profile?id=5e70814b7adb803e5a5f7563aa078e1f&encoded=0&v=paper_preview&mkt=zh-cn [7] KASPER D. HANSEN, WU Z J, et al. Sequencing technology does not eliminate biological variability[J]. Nature Biotechnology, 2011, 572-573. http://cn.bing.com/academic/profile?id=3309a6845ad7f0790836654d25f18185&encoded=0&v=paper_preview&mkt=zh-cn [8] ALTSCHUL S F, MADDEN T L, ZHANG J, et al. Gapped BLAST and PSI BLAST: A New Generation of Protein Database Search Programs[J]. Nucleic Acids Research, 1997, 25(17): 3389-3402. doi: 10.1093/nar/25.17.3389 [9] DENG Y Y, LI J Q, WU S F, et al. Integrated nr Database in Protein Annotation System and Its Localization[J]. Computer Engineering, 2006, 32(5):71-74. http://cn.bing.com/academic/profile?id=427de9518225b28b8d23de80d088577d&encoded=0&v=paper_preview&mkt=zh-cn [10] APWEILER R, BAIROCH A, WU CH, et al. UniProt: the universal protein knowledgebase[J]. Nucleic Acids Research, 2004, 32: D115-D119. doi: 10.1093/nar/gkh131 [11] ASHBURNER M, BALL C A, BLAKE J A, et al. Gene ontology: tool for the unification of biology[J]. Nature Genetics, 2000, 25(1): 25-29. doi: 10.1038/75556 [12] TATUSOV R L, GALPERIN M Y, NATALE D A. The COG database: a tool for genome scale analysis of protein functions and evolution[J]. Nucleic Acids Research, 2000, 28(1):33-36. doi: 10.1093/nar/28.1.33 [13] KOONIN E V, FEDOROVA N D, JACKSON J D, et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes[J]. Genome Biology, 2004, 5(2): R7. doi: 10.1186/gb-2004-5-2-r7 [14] KERRIGAN R W, CHALLEN M P, Burton K S. Agaricus bisporus genome sequence: a commentary[J]. Fungal Genetics and Biology, 2013, 55:2-5. doi: 10.1016/j.fgb.2013.03.002 [15] 吴小梅, 张昕, 李南羿.双孢蘑菇子实体不同发育时期的转录组分析[J].菌物学报, 2017, 36(2): 193-203. http://www.cnki.com.cn/Article/CJFDTotal-FJNX201803012.htm [16] CHEN M Y, LIAO J H, LI H R, et al. iTRAQ-MS/MS proteomic analysis reveals differentially expressed proteins during post-harvest maturation of the white button mushroom Agaricus bisporus[J]. Current Microbiology, 2017, 74(5):641-649. doi: 10.1007/s00284-017-1225-y [17] De GROOT P W, SCHAAP P J, SONNENBERG A S, et al. The Agaricus bisporus hyp A gene encodes a hydrophobin and specifically accumulates in peel tissue of mushroom caps during fruit body development[J]. Journal of Molecular Biology, 1996, 257(5):1008-1018. doi: 10.1006/jmbi.1996.0219 [18] De GROOT P W J, ROEVEN R T P, VAN GRIENSVEN LJLD, et al. Different temporal and spatial expression of two hydrophobin-encoding genes of the edible mushroom Agaricus bisporus[J]. Microbiology, 1999, 145(5):1105-1113. doi: 10.1099/13500872-145-5-1105 [19] LUGONES L G, BOSSCHER J S, SCHOLTMEYER K, et al. An abundant hydrophobin(ABH1) forms hydrophobic rodlet layers in Agaricus bisporus fruiting bodies[J]. Microbiology, 1996, 142(5):1321-1329. doi: 10.1099/13500872-142-5-1321 -
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