Chromosome-level genome assembly of an agricultural pest, the rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera)

A chromosome-level genome assembly of beet webworm, Loxostege sticticalis Linnaeus (Lepidoptera: Pyralidae)

The beet webworm, Loxostege sticticalis Linnaeus (Lepidoptera, Pyralidae), is a major pest in agriculture and livestock production. However, the L. sticticalis genome has not yet been sequenced, limiting exploration of its biological features and population genetics. In this study, the genome of L. sticticalis was sequenced on the Illumina Novaseq. 6000 and PacBio Sequel II platforms, and chromosome conformation capture (Hi-C) methods were used to generate the high-quality chromosome-level genome, assessed at 98.7% by the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool. The L. sticticalis genome showed an assembly of 485.9 Mb with a contig N50 of 16.4 Mb, a scaffold N50 of 16.6 Mb, and a GC content of 37.85%, with over 98.67% of the assembled bases located on 31 chromosomes. Repeat sequences accounted for 41.71% of the genome and 15 913 protein-coding genes were identified. Comparison of the genome of L. sticticalis with other closely related species indicated high chromosomal synteny. The sequencing of this genome contributes to research on the genetics and evolution of the Lepidoptera.

Chromosome-level genome assembly of Parotis chlorochroalis (Lepidoptera: Crambidae: Spilomelinae)

Parotis Hübner, 1831 is a genus within the family Crambidae, which is recognized as one of the most diverse families of Lepidoptera. Species within the genus Parotis can be readily distinguished from other closely related genera by their distinctive green or yellow-green body coloration. However, the genus Parotis has received relatively limited research attention, and the scarcity of genome-wide molecular resources has impeded a more comprehensive understanding of its evolution, adaptation, and phylogenetic relationships. This study reports the first genome assembly for Parotis chlorochroalis (Hampson, 1912), generated through PacBio Hi-Fi and Hi-C sequencing technologies. The assembled genome has a size of 456.23 Mb, comprising 31 chromosomes. Approximately 181.82 Mb, which constitutes 39.85% of the genome, has been identified as repetitive sequences. The genome assembly includes 16,299 protein-coding genes, of which 94.82% have been functionally annotated. This chromosome-level genome assembly not only advance understanding of P. chlorochroalis but also has the potential to facilitate genomic studies of other lepidopteran species.

Deep Insight into the genome of a major rice pest, Scripophaga incertulas

The yellow stem borer, Scripophaga incertulas (Crambidae, Lepidoptera), is a highly destructive pest damaging rice crops. Here, we combined Illumina, PacBio sequencing and Hi-C scaffolding to generate a high-quality chromosome-level genome assembly of S. incertulas. We initially obtained an 839.78 Mb assembly with scoffold N50 of 1.13 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis demonstrated that this genome assembly has a high-level completeness of 97.5% gene coverage. The assembly contained 45.67% repetitive sequences (383.50 Mb), and has been annotated with 19,874 protein-coding genes. Next, 3,369 scaffolds were anchored to 26 chromosomes, resulting in an increase of the N50 to 32.16 Mb. Our research provides insights into the evolution and ecology of S. incertulas, offering valuable resources for future pest management.

Chromosome-level genome assembly and sex chromosome identification of the pink stem borer, Sesamia inferens (Lepidoptera: Noctuidae)

The pink stem borer, Sesamia inferens Walker (Lepidoptera: Noctuidae), is one of the most notorious pest insects of rice and maize crops in the world. Here, we generated a high-quality chromosome-level genome assembly of S. inferens, using a combination of Illumina, PacBio HiFi and Hi-C technologies. The total assembly size was 973.18 Mb with a contig N50 of 33.39 Mb, anchored to 31 chromosomes, revealing a karyotype of 30 + Z. The BUSCO analysis indicated a high completeness of 98.90% (n = 5286), including 5172 (97.8%) single-copy BUSCOs and 58 (1.1%) duplicated BUSCOs. The genome contains 58.59% (564.58 Mb) repeat elements and 26628 predicted protein-coding genes. The chromosome-level genome assembly of S. inferens provides in-depth knowledge and will be a helpful resource for the Lepidoptera and pest control research communities.

Multiple independent origins of the female W chromosome in moths and butterflies

Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of the lepidopteran W chromosome remains poorly understood. Here, we assemble the genome from females down to the chromosome level of a model insect (Bombyx mori) and identify a W chromosome of approximately 10.1 megabase using a newly developed tool. In addition, we identify 3593 genes that were not previously annotated in the genomes of B. mori. Comparisons of 21 lepidopteran species (including 17 ZW and four Z0 systems) and three trichopteran species (Z0 system) reveal that the formation of Ditrysia W involves multiple mechanisms, including previously proposed canonical and noncanonical models, as well as a newly proposed mechanism called single-Z turnover. We conclude that there are multiple independent origins of the W chromosome in the Ditrysia (most moths and all butterflies) of Lepidoptera.

A chromosome-level genome assembly of tomato pinworm, Tuta absoluta

The tomato pinworm, Tuta absoluta, or Phthorimaea absouta, is native to South America, but quickly spread to other regions of world, including Europe, Africa, and Asia, devastating to global tomato production. However, a lack of high-quality genome resources makes it difficult to understand its high invasiveness and ecological adaptation. Here, we sequenced the genome of the tomato pinworm using Nanopore platforms, yielding a genome assembly of 564.5 Mb with contig N50 of 3.33 Mb. BUSCO analysis demonstrated that this genome assembly has a high-level completeness of 98.0% gene coverage. In total, 310 Mb are repeating sequences accounting for 54.8% of genome assembly, and 21,979 protein-coding genes are annotated. Next, we used the Hi-C technique to anchor 295 contigs to 29 chromosomes, yielding a chromosome-level genome assembly with a scaffold N50 of 20.7 Mb. In sum, the high-quality genome assembly of the tomato pinworm is a useful gene resource that contributes to a better understanding of the biological characteristics of its invasiveness and will help in developing an efficient control policy.

An Efficient Feature Selection Algorithm for Gene Families Using NMF and ReliefF

Gene families, which are parts of a genome's information storage hierarchy, play a significant role in the development and diversity of multicellular organisms. Several studies have focused on the characteristics of gene families, such as function, homology, or phenotype. However, statistical and correlation analyses on the distribution of gene family members in the genome have yet to be conducted. Here, a novel framework incorporating gene family analysis and genome selection based on NMF-ReliefF is reported. Specifically, the proposed method starts by obtaining gene families from the TreeFam database and determining the number of gene families within the feature matrix. Then, NMF-ReliefF is used to select features from the gene feature matrix, which is a new feature selection algorithm that overcomes the inefficiencies of traditional methods. Finally, a support vector machine is utilized to classify the acquired features. The results show that the framework achieved an accuracy of 89.1% and an AUC of 0.919 on the insect genome test set. We also employed four microarray gene data sets to evaluate the performance of the NMF-ReliefF algorithm. The outcomes show that the proposed method may strike a delicate balance between robustness and discrimination. Additionally, the proposed method's categorization is superior to state-of-the-art feature selection approaches.

Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees

The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.

A chromosome-level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)

Paracymoriza distinctalis is a semiaquatic lepidopteran insect, which is of great value for studying the differentiation of the Pyraloidea superfamily. However, the understanding of heredity, evolution, and functional genomics of P. distinctalis are limited by few genome-wide resources. Here, we applied PacBio sequencing and the chromosome capture technique to assemble the first P. distinctalis genome from a single female individual. The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb. Approximately 576.37 Mb, accounting for 48.93% of the genome, was identified as repeats. The genome comprises 39,003 protein-coding genes, 66.56% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of P. distinctalis and Chilo suppressalis lived ~83.5 million years ago. This chromosome-level genome assembly work is not only conducive to the understanding of P. distinctalis, but also may promote the study of the genomes of other lepidopteran species.