Genetic and genomic analysis for cocoon yield traits in silkworm.

Domestic species provides a powerful model for examining genetic mechanisms in the evolution of yield traits. The domestic silkworm (Bombyx mori) is an important livestock species in sericulture. While the mechanisms controlling cocoon yield are largely unknown. Here, using B. mori and its wild relative B. mandarina as intercross parents, 100 BC1 individuals were sequenced by restriction site-associated DNA sequencing (RAD-Seq). The linkage map contained 9,632 markers was constructed. We performed high-resolution quantitative trait locus (QTL) mapping for four cocoon yield traits. A total of 11 QTLs were identified, including one yield-enhancing QTL from wild silkworm. By integrating population genomics and transcriptomic analysis with QTLs, some favourable genes were revealed, including 14 domestication-related genes and 71 differentially expressed genes (DEGs) in the fifth-instar larval silk gland transcriptome between B. mori and B. mandarina. The relationships between the expression of two important candidate genes (KWMTBOMO04917 and KWMTBOMO12906) and cocoon yield were supported by quantitative real-time PCR (qPCR). Our results provide some new insights into the molecular mechanisms of complex yield traits in silkworm. The combined method might be an efficient approach for identifying putative causal genes in domestic livestock and wild relatives.

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication.

Long-term domestication and selective breeding have increased the silk yield of the domestic silkworm (Bombyx mori) by several times the amount of the silk yield of its wild ancestor (Bombyx mandarina). However, little is known about the molecular mechanisms behind the increase in silk yield during domestication. Based on dynamic patterns of functional divergence in the silk gland between domestic and wild silkworms, we found that at early and intermediate stages of silk gland development, the up-regulated genes of the domestic silkworm were mainly involved in DNA integration, nucleic acid binding, and transporter activity, which are related to the division and growth of cells. This has led to the posterior silk gland (PSG) of the domestic silkworm having significantly more cells ("factories" of fibroin protein synthesis) than that of the wild silkworm. At the late stage of silk gland development, the up-regulated genes in the domestic silkworm was enriched in protein processing and ribosome pathways, suggesting protein synthesis efficiency is greatly improved during silkworm domestication. While there was an increase in fibroin protein synthesis, the production of sericin protein was simultaneously reduced in the silk gland of the domestic silkworm. This reflects that domestic and wild silkworms have been under different selection pressures. Importantly, we found that the network co-expressed with the silk-coding genes of the domestic silkworm was larger than that of the wild silkworm. Furthermore, many more genes co-expressed with silk-coding genes in the domestic silkworm were subjected to artificial selection than those in the wild silkworm. Our results revealed that the increase of silk yield during silkworm domestication is involved in improvement of a biological system which includes not only expansion of "factories" (cells of PSG) of protein synthesis, but also a high expression of silk-coding genes and silk production-related genes such as biological energy, transport, and ribosome pathway genes.

Evidence of peripheral olfactory impairment in the domestic silkworms: insight from the comparative transcriptome and population genetics.

BACKGROUND: The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori has changed greatly since domestication from B. mandarina, and its olfactory response to environmental odorants clearly decreased. However, the mechanisms that result in the olfactory impairment are largely unknown. RESULTS: The antennal transcriptomes were compared between the domestic and wild silkworms. Comparison of the same sex between the domestic and wild silkworms revealed 1410 and 1173 differentially expressed genes (DEGs) in males and females, respectively. To understand the olfactory impairment, we mainly focused on the olfactory-related genes. In total, 30 olfactory genes and 19 odorant-degrading enzymes (ODEs) showed differential expression in the two comparisons, in which 19 and 14 were down-regulated in the domestic silkworm, respectively. Based on population genomic data, the down-regulated odorant receptors (ORs) showed a higher ratio of unique non-synonymous polymorphisms to synonymous polymorphisms (N/S ratio) in the domestic populations than that in the wild silkworms. Furthermore, one deleterious mutation was found in OR30 of the domestic population, which was located in transmembrane helix 6 (TM6). CONCLUSIONS: Our results suggested that down-regulation of the olfactory-related genes and relaxed selection might be the major reasons for olfactory impairment of the domestic silkworm reared completely indoor environment. Reversely, wild silkworm may increase expression and remove deleterious polymorphisms of olfactory-related genes to retain sensitive olfaction.

Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes.

BACKGROUND: Transposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2.5-Mb emphasizes the need for biologists to rethink the fundamental nature of the relationship between viruses and cellular life. RESULTS: Herein, we performed the first comprehensive analysis of miniature inverted-repeat transposable elements (MITEs) in the 5170 viral genomes for which sequences are currently available. Four hundred and fifty one copies of ten miniature inverted-repeat transposable elements (MITEs) were found and each MITE had reached relatively large copy numbers (some up to 90) in viruses. Eight MITEs belonging to two DNA superfamilies (hobo/Activator/Tam3 and Chapaev-Mirage-CACTA) were for the first time identified in viruses, further expanding the organismal range of these two superfamilies. TEs may play important roles in shaping the evolution of pandoravirus genomes, which were here found to be very rich in MITEs. We also show that putative autonomous partners of seven MITEs are present in the genomes of viral hosts, suggesting that viruses may borrow the transpositional machinery of their cellular hosts' autonomous elements to spread MITEs and colonize their own genomes. The presence of seven similar MITEs in viral hosts, suggesting horizontal transfers (HTs) as the major mechanism for MITEs propagation. CONCLUSIONS: Our discovery highlights that TEs contribute to shape genome evolution of pandoraviruses. We concluded that as for cellular organisms, TEs are part of the pandoraviruses' diverse mobilome.

Identification and comparison of long non-coding RNAs in the silk gland between domestic and wild silkworms.

Under long-term artificial selection, the domestic silkworm (Bombyx mori) has increased its silk yield tremendously in comparison with its wild progenitor, Bombyx mandarina. However, the molecular mechanism of silk yield increase is still unknown. Comparative analysis of long non-coding RNAs (lncRNAs) may provide some insights into understanding this phenotypic variation. In this study, using RNA sequencing technology data of silk gland in domestic and wild silkworms, we identified 599 lncRNAs in the silk gland of the silkworm. Compared with protein-coding genes, the silk gland lncRNA genes tend to have fewer exon numbers, shorter transcript length and lower GC-content. Moreover, we found that three lncRNA genes are significantly and differentially expressed between domestic and wild silkworms. The potential targets of two differentially expressed lncRNAs (DELs) (dw4sg_0040 and dw4sg_0483) and the expression-correlated genes with the two DELs are mainly enriched in the related processes of silk protein translation. This implies that these DELs may affect the phenotypic variation in silk yield between the domestic and wild silkworms through the post-transcriptional regulation of silk protein.

iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects.

Miniature inverted-repeat transposable elements (MITEs) have attracted much attention due to their widespread occurrence and high copy numbers in eukaryotic genomes. However, the systematic knowledge about MITEs in insects and other animals is still lacking. In this study, we identified 6012 MITE families from 98 insect species genomes. Comparison of these MITEs with known MITEs in the NCBI non-redundant database and Repbase showed that 5701(∼95%) of 6012 MITE families are novel. The abundance of MITEs varies drastically among different insect species, and significantly correlates with genome size. In general, larger genomes contain more MITEs than small genomes. Furthermore, all identified MITEs were included in a newly constructed database (iMITEdb) (http://gene.cqu.edu.cn/iMITEdb/), which has functions such as browse, search, BLAST and download. Overall, our results not only provide insight on insect MITEs but will also improve assembly and annotation of insect genomes. More importantly, the results presented in this study will promote studies of MITEs function, evolution and application in insects. DATABASE URL: http://gene.cqu.edu.cn/iMITEdb/.

BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori.

BACKGROUND: Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). DESCRIPTION: In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. CONCLUSIONS: We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .

Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms.

BACKGROUND: Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the mRNA deep sequencing (RNA-seq) approach to identify the differentially expressed genes (DEGs) in the transcriptomes of the median/posterior silk glands of two domestic and two wild silkworms. RESULTS: The results indicated that about 58% of the total genes were expressed (reads per kilo bases per million reads (RPKM) ≥ 1) in each silkworm. Comparisons of the domestic and wild silkworm transcriptomes revealed 32 DEGs, of which 16 were up-regulated in the domestic silkworms compared with in the wild silkworms, and the other 16 were up-regulated in the wild silkworms compared with in the domestic silkworms. Quantitative real-time polymerase chain reaction (qPCR) was performed for 15 randomly selected DEGs in domestic versus wild silkworms. The qPCR results were mostly consistent with the expression levels determined from the RNA-seq data. Based on a Gene Ontology (GO) enrichment analysis and manual annotation, five of the up-regulated DEGs in the wild silkworms were predicted to be involved in immune response, and seven of the up-regulated DEGs were related to the GO term "oxidoreductase activity", which is associated with antioxidant systems. In the domestic silkworms, the up-regulated DEGs were related mainly to tissue development, secretion of proteins and metabolism. CONCLUSIONS: The up-regulated DEGs in the two domestic silkworms may be involved mainly in the highly efficient biosynthesis and secretion of silk proteins, while the up-regulated DEGs in the two wild silkworms may play more important roles in tolerance to pathogens and environment adaptation. Our results provide a foundation for understanding the molecular mechanisms of the silk production difference between domestic and wild silkworms.