title: New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi.
abstract: BACKGROUND
  To date, biologists have discovered a large amount of valuable information from assembled genomes, but the abundant microbial data that is hidden in the raw genomic sequence data of plants and animals is usually ignored. In this study, the richness and composition of fungal community were determined in the raw genomic sequence data of Ceratosolen solmsi (RGSD-CS).
  
  
  RESULTS
  To avoid the interference from sequences of C. solmsi, the unmapped raw data (about 17.1%) was obtained by excluding the assembled genome of C. solmsi from RGSD-CS. Comparing two fungal reference datasets, internal transcribed spacer (ITS) and large ribosomal subunit (LSU) of rRNA, the ITS dataset discovered a more diverse fungal community and was therefore selected as the reference dataset for evaluating the fungal community based on the unmapped raw data. The threshold of 95% sequence identity revealed many more matched fungal reads and fungal richness in the unmapped raw data than those by identities above 95%. Based on the threshold of 95% sequence identity, the fungal community of RGSD-CS was primarily composed of Saccharomycetes (88.4%) and two other classes (Agaricomycetes and Sordariomycetes, 8.3% in total). Compared with the fungal community of other reported fig wasps, Agaricomycetes and Eurotiomycetes were found to be unique to C. solmsi. In addition, the ratio of total fungal reads to RGSD-CS was estimated to be at least 4.8 × 10(-3), which indicated that a large amount of fungal data was contained in RGSD-CS. However, rarefaction measure indicated that a deeper sequencing coverage with RGSD-CS was required to discover the entire fungal community of C. solmsi.
  
  
  CONCLUSIONS
  This study investigated the richness and composition of fungal community in RGSD-CS and provided new insights into the efficient study of microbial diversity using raw genomic sequence data.
authors.affiliation: College of Plant Protection, Shandong Agricultural University, Tai'an, China. nlhnq55@163.com.|Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. nlhnq55@163.com.|College of Environment, Hohai University, Nanjing, China. nlhnq55@163.com.
authors.forename: Li-Hua
authors.initials: LH
authors.lastname: Niu
authors.affiliation: College of Plant Protection, Shandong Agricultural University, Tai'an, China. hanhantianzi@163.com.
authors.forename: Xiu-Feng
authors.initials: XF
authors.lastname: Song
authors.affiliation: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. heshunmin@gmail.com.
authors.forename: Shun-Min
authors.initials: SM
authors.lastname: He
authors.affiliation: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. zhpn1024@163.com.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.affiliation: College of Plant Protection, Shandong Agricultural University, Tai'an, China. nxwang@sdau.edu.cn.
authors.forename: Ning-Xin
authors.initials: NX
authors.lastname: Wang
authors.affiliation: College of Environment, Hohai University, Nanjing, China. envly@hhu.edu.cn.
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Plant Protection, Shandong Agricultural University, Tai'an, China. huangdw@ioz.ac.cn.|Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. huangdw@ioz.ac.cn.
authors.forename: Da-Wei
authors.initials: DW
authors.lastname: Huang
mesh_terms: D000818:Animals; D058448:Biota; D016000:Cluster Analysis; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D030681:Ficus / Q000469:parasitology; D005658:Fungi / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D017422:Sequence Analysis, DNA; D014863:Wasps / Q000382:microbiology*
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D012335:RNA, Ribosomal; C065096:RNA, ribosomal, 26S