Reference Transcriptome Data in Silkworm Bombyx mori

Abstract

Herein, we performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. The sequences were mapped onto the reference genome assembly and the reference transcriptome data were successfully constructed. The reference data provided a nearly complete sequence for sericin-1, a major silk gene with a complex structure. We also markedly improved the gene model for other genes. The transcriptomic expression was investigated in each tissue and a number of transcripts were identified that were exclusively expressed in tissues such as the testis. Transcripts strongly expressed in the midgut formed tight genomic clusters, suggesting that they originated from tandem gene duplication. Transcriptional factor genes expressed in specific tissues or the silk gland subparts were also identified. We successfully constructed reference transcriptome data in the silkworm and found that a number of transcripts showed unique expression profiles. These results will facilitate basic studies on the silkworm and accelerate its applications, which will contribute to further advances in lepidopteran and entomological research as well as the practical use of these insects.

Co-Expression Network and Time-Course Expression Analyses to Identify Silk Protein Regulatory Factors in Bombyx mori

“…Although SGF3 , as with SGF1 , is also involved in regulating sericin1 expression [ 8 , 9 , 10 ], it is possible that KWMTBOMO02915 ( Figure 2 D) regulates sericin3 expression as its expression pattern was similar to that of sericin3 in the A-MSG ( Figure 3 C,F). Furthermore, KWMTBOMO02915 was already recognized as MSG-specific expression TF in a previous study [ 24 ]. The expression level of the histone superfamily gene KWMTBOMO12108 decreased in the later period of last instar, and it was similar to that of sericin2 .…”

“…For co-expression network analysis with networkz , we used transcript-level transcripts per million (TPM) values as expression data of two RNA-seq data series, which were used for the assembly and verification of the current reference transcriptome dataset of B. mori in our previous study [ 24 ] The first RNA-seq data series (SRA Run ID: DRR068893-068895 and DRR095105-095116) was obtained from the fat body (FB), midgut (MG), MT, whole SG (SG), and TT of the o751 strain last instar larvae on third day ( Table 1 ) [ 21 , 22 , 23 ]. The second RNA-seq data series (SRA Run ID: DRR186474-186503) was obtained from the aforementioned five SG regions (ASG, A-MSG, M-MSG, P-MSG, and PSG), FB, MG, MT, TT, and OV of p50T strain last instar larvae on third day ( Table 1 ) [ 24 ]. The transcript-level TPM expression data that were used in this study are available at “expression data of each transcript in multiple tissues” in the study by Yokoi et al 2021 (doi: 10.18908/lsdba.nbdc02443-002.V001), in which 51,926 transcripts were used as reference sequences for TPM calculation [ 24 ].…”

“…The second RNA-seq data series (SRA Run ID: DRR186474-186503) was obtained from the aforementioned five SG regions (ASG, A-MSG, M-MSG, P-MSG, and PSG), FB, MG, MT, TT, and OV of p50T strain last instar larvae on third day ( Table 1 ) [ 24 ]. The transcript-level TPM expression data that were used in this study are available at “expression data of each transcript in multiple tissues” in the study by Yokoi et al 2021 (doi: 10.18908/lsdba.nbdc02443-002.V001), in which 51,926 transcripts were used as reference sequences for TPM calculation [ 24 ]. Herein we used the same transcript ID as that of reference transcript sequences.…”

“…Accordingly, we developed a fast C++-based tool to quickly process large expression datasets. Co-expression network analysis was performed using published transcriptome data [ 21 , 22 , 23 , 24 ] comprising five SG regions [anterior SG (ASG), anterior-middle SG (A-MSG), middle-middle SG (M-MSG), posterior-middle SG (P-MSG), and posterior SG (PSG)], Malpighian tubule (MT), testis (TT), and ovary (OV). A total of six silk protein genes [ sericin1 , sericin2 , sericin3 , fibroin heavy-chain ( fibroin-H ), fibroin light-chain ( fibroin-L ), and fibrohexamerin ( P25 )] were selected as target genes to search for regulatory factors.…”

Advances in Editing Silkworms (Bombyx mori) Genome by Using the CRISPR-Cas System

“…The level of attention received as a model experimental organism increased, since several groups made available B. mori's genome data [91]. Various mutant strains have been described and the genetic analysis confirmed the numerous genetic traits.…”