The genome sequence of Samia ricini, a new model species of lepidopteran insect

Midgut serine proteinases participate in dietary adaptations of the castor (Eri) silkworm Samia ricini Anderson transferred from Ricinus communis to an ancestral host, Ailanthus excelsa Roxb

Dietary change influenced the life-history traits, nutritional utilization, and midgut serine proteinases in the larvae of the domesticated polyphagous S. ricini, transferred from R. communis (common name: castor; family Euphorbiaceae; the host plant implicated in its domestication) to A. excelsa (common name: Indian tree of heaven; family Simaroubaceae; an ancestral host of wild Samia species). Significantly higher values for fecundity and body weight were observed in larvae feeding on R. communis (Scr diet), and they took less time to reach pupation than insects feeding on A. excelsa (Scai diet). Nevertheless, the nutritional index for efficiency of conversion of digested matter (ECD) was similar for larvae feeding on the two plant species, suggesting the physiological adaptation of S. ricini (especially older instars) to an A. excelsa diet. In vitro protease assays and gelatinolytic zymograms using diagnostic substrates and protease inhibitors revealed significantly elevated levels (p ≤ 0.05) of digestive trypsins, which may be associated with the metabolic costs influencing slow growth in larvae feeding on A. excelsa. RT-PCR with semidegenerate serine proteinase gene-specific primers, and cloning and sequencing of 3' cDNA ends identified a large gene family comprising at least two groups of putative chymotrypsins (i.e., Sr I and Sr II) resembling invertebrate brachyurins/collagenases with wide substrate specificities, and five groups of putative trypsins (i.e., Sr III, Sr IV, Sr V, Sr VII, and Sr VIII). Quantitative RT-PCR indicated that transcripts belonging to the Sr I, Sr III, Sr IV, and Sr V groups, especially the Sr IV group (resembling achelase I from Lonomia achelous), were expressed differentially in the midguts of fourth instars reared on the two plant species. Sequence similarity indicated shared lineages with lepidopteran orthologs associated with expression in the gut, protein digestion, and phytophagy. The results obtained are discussed in the context of larval serine proteinases in dietary adaptations, domestication, and exploration of new host plant species for commercial rearing of S. ricini.

SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species

We introduce SilkBase as an integrated database for transcriptomic and genomic resources of the domesticated silkworm Bombyx mori and related species. SilkBase is the oldest B. mori database that was originally established as the expressed sequence tag database since 1999. Here, we upgraded the database by including the datasets of the newly assembled B. mori complete genome sequence, predicted gene models, bacterial artificial chromosome (BAC)-end and fosmid-end sequences, complementary DNA (cDNA) reads from 69 libraries, RNA-seq data from 10 libraries, PIWI-interacting RNAs (piRNAs) from 13 libraries, ChIP-seq data of 9 histone modifications and HP1 proteins and transcriptome and/or genome data of four B. mori-related species, i.e. Bombyx mandarina, Trilocha varians, Ernolatia moorei and Samia ricini. Our new integrated genome browser easily provides a snapshot of tissue- and stage-specific gene expression, alternative splicing, production of piRNAs and histone modifications at the gene locus of interest. Moreover, SilkBase is useful for performing comparative studies among five closely related lepidopteran insects.

Database URL: https://silkbase.ab.a.u-tokyo.ac.jp

Integration of Transcriptomic and Proteomic Analyses Reveals New Insights into the Regulation of Immune Pathways in Midgut of Samia ricini upon SariNPV Infection

Simple Summary

SariNPV is one of the main pathogens of Samia ricini and its infection of Samia ricini sericulture has caused significant economic losses to society. In this study, we aim to reveal the molecular mechanism of pathogen–host interactions in SariNPV-infected S. ricini through transcriptomic and proteomic analyses. Using RNA-sequencing and iTRAQ, we mapped the differentially expressed genes (DEGs) and proteins (DEPs) that are involved in the immune responses of S. ricini upon virus invasion. Based on our analyses, we identified specific DEGs and DEPs that are involved in various essential biological signaling pathways and immune-related pathways upon SariNPV invasion. These DEGs and DEPs play an important role in triggering host immune responses to pathogens. Our study provides molecular insights into host immune responses regarding pathogen invasion, in particular, the immune response mechanism and network of S. ricini in response to SariNPV infection.

Abstract

Samia ricini nucleopolyhedrovirus (SariNPV) is one of the main pathogens of S. ricini sericulture and its infection causes severe impacts on economic sericulture development. To explore and reveal the molecular mechanisms of S. ricini in response to SariNPV infection, we employed RNA sequencing (RNA-seq), adopting isobaric tags for relative and absolute quantitation (iTRAQ), and carried out combination analysis of the obtained differentially expressed genes (DEGs) and proteins (DEPs). Through transcriptome sequencing, a total of 2535 DEGs were detected, and with iTRAQ, 434 DEPs with significant expression difference were identified. Through correlation analysis, we found that the expression trends of 116 differentially expressed proteins were the same as those of differentially expressed genes (including 106 up-regulated and 10 down-regulated). Twenty-five key differentially expressed genes (proteins) involved in several signaling and immune related pathways (mainly involving Toll, Imd, Jak-STAT and Wnt signaling pathways, as well as other immune related pathways) were screened through real-time quantitative PCR. Our results, not only provide insights into the pathogenic mechanism of SariNPV infection in ricin silkworm and the immune response mechanism within the host, but also provide a significant contribution for identifying and preventing diseases caused by SariNPV.

TSEBRA: transcript selector for BRAKER

BACKGROUND

BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence and, then predicts protein-coding genes in genomic sequences using both the extrinsic evidence and statistical models. For training and prediction, BRAKER1 and BRAKER2 incorporate complementary extrinsic evidence: BRAKER1 uses only RNA-seq data while BRAKER2 uses only a database of cross-species proteins. The BRAKER suite has so far not been able to reliably exceed the accuracy of BRAKER1 and BRAKER2 when incorporating both types of evidence simultaneously. Currently, for a novel genome project where both RNA-seq and protein data are available, the best option is to run both pipelines independently, and to pick one, likely better output. Therefore, one or another type of the extrinsic evidence would remain unexploited.

RESULTS

We present TSEBRA, a software that selects gene predictions (transcripts) from the sets generated by BRAKER1 and BRAKER2. TSEBRA uses a set of rules to compare scores of overlapping transcripts based on their support by RNA-seq and homologous protein evidence. We show in computational experiments on genomes of 11 species that TSEBRA achieves higher accuracy than either BRAKER1 or BRAKER2 running alone and that TSEBRA compares favorably with the combiner tool EVidenceModeler.

CONCLUSION

TSEBRA is an easy-to-use and fast software tool. It can be used in concert with the BRAKER pipeline to generate a gene prediction set supported by both RNA-seq and homologous protein evidence.

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing

We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called mandibulate archaic moths (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 Ma and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly contiguous genome with a contig N50 of nearly 17 Mb. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.