Background & Summary

The pine wilt disease is currently considered one of the most serious threats to pine forests worldwide1,2,3. This disease is caused by the pinewood nematode Bursaphelenchus xylophilus (Steiner and Buhrer) (Nematoda: Aphelenchoididae), an invasive species originally from North America2. The natural spread of pinewood nematode usually requires insect vectors4. The longhorn beetles from the Monochamus (Coleoptera: Cerambycidae) are the primary vectors of the pinewood nematode5,6,7. The Japanese sawyer beetle Monochamus alternatus (Hope) (Coleoptera: Cerambycidae: Lamiinae) is an effective vector of the pinewood nematode8. The M. alternatus can cause damage directly to various species of pine trees from the genera Pinus, Cedrus, Abies, Picea, and Larix4. This beetle is widely distributed in Japan, Korea, Laos, Vietnam, and the surrounding countries9,10. Single M. alternatus can harbor, on average, 15,000 and up to 280,000 pinewood nematodes in its tracheal system11,12. Monochamus saltuarius is another species that was reported as the vector beetle of pinewood nematode in Japan, Europe, and China. It was first reported to transmit the pinewood nematode to native Pinus species in Liaoning Province, China13. It is crucial to understand the ecology and genetics of M. alternatus and how it transmits pinewood nematodes14,15. The genome of M. saltuarius has been sequenced and assembled16. However, the genome of M. alternatus has yet to be determined. Bridging this knowledge gap will greatly aid our control efforts against M. alternatus and pine wilt disease17.

In this study, we assembled the chromosome-level genome of M. alternatus using a combination of Nanopore, Illumina short-read sequencing, and chromosome conformation capture (Hi-C) technologies to provide genomic resources for future investigations on the ecology, genetics, and evolution of the M. alternatus and the interaction between the pinewood nematode and its insect vector.

Methods

Sample preparation

Samples of M. alternatus were from a laboratory strain reared at the Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China. This strain was reared for about 30 generations in the laboratory. A single female adult was used to construct libraries of Illumina short read, Oxford Nanopore Technology (ONT) long read sequencing, and Hi-C. The samples were starved for 24 hours, and the guts of the adults were removed to minimize contamination from gut microbes. In addition, we collected three larvae, pupae, and adults of M. alternatus for transcriptome sequencing. All samples were frozen in liquid nitrogen and stored at −80 °C until further usage.

Genomic DNA and RNA sequencing

For short-read sequencing, genomic DNA was extracted using the QIAGEN® Genomic DNA extraction kit (Qiagen, Hilden, Germany) according to the standard operating procedure provided by the manufacturer. The pair-end library with an insert size of about 300 bp was prepared using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, ND607, Nanning, China) and sequenced on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). We obtained 42.5 Gb Illumina short reads (Table 1).

Table 1 Library sequencing data and methods used in this study to assemble the Monochamus alternatus genome.
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For long-read sequencing, high molecular weight genomic DNA was isolated using the QIAGEN® Genomic DNA extraction kit (Qiagen, Hilden, Germany) according to the standard operating procedure provided by the manufacturer. A total of 3–4 μg DNA was used as input material for the ONT library preparation. Long DNA fragments were selected using the PippinHT system (Sage Science, USA). The A-ligation reaction was conducted with the NEBNext Ultra II End Repair/dA-tailing Kit (Ipswich, MA, USA). The adapter in the SQK-LSK109 (Oxford Nanopore Technologies, UK) was used for further ligation reaction. About 700 ng DNA library was constructed and performed on a Nanopore PromethION sequencer instrument (Oxford Nanopore Technologies, UK) at the GrandOmics Biosciences Co., Ltd. (Wuhan, China), and 142.7 Gb long reads were generated (Table 1).

For Hi-C sequencing, the library was prepared according to the standard protocol described by Belton with minor modifications18. An adult of M. alternatus was cut into pieces and mixed with 2% formaldehyde solution for cross-linking. Glycine (2.5 M) was added to stop this reaction, and the sample was homogenized to separate the nuclei. The purified nuclei were dissolved in SDS and incubated at 65 °C for 10 min. After quenching the SDS with Triton X-100, the sample was digested with Dpn II and marked by incubating with biotin-14-dCTP. Biotin from nonligated DNA ends was removed by T4 DNA polymerase. Then, the Hi-C library was prepared by Truseq Nano DNA HT Kit (Illumina, USA) and sequenced on the Illumina HiSeq platform with paired-end 150-bp reads (Illumina, San Diego, CA, USA) at Annoroad Gene Technology Co., Ltd. (Beijing, China). A total of 81.7 Gb (106 × coverage) of clean data was generated (Table 1).

For transcriptome sequencing, total RNA was extracted from a single M. alternatus (larva, pupa, and adult, respectively) using the RNAprep Pure Tissue Kit (Tiangen, China). Library was constructed using a TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) and sequenced on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) with the paired-end mode at GrandOmics Biosciences Co., Ltd. (Wuhan, China). A total of 18.9 Gb transcriptome data was obtained (Table 1).

Estimation of genomic characteristics

The Illumina raw reads were checked and filtered using Trimmomatic version 0.39-219 to discard reads with adaptors, unknown nucleotides (Ns), or >20% low-quality bases. Genome size, heterozygosity, and duplication were estimated by using Jellyfish version 2.2.1020 and GenomeScope version 2.021 based on the 17-mer depth distribution. The estimated genome size was 667 Mb, with a heterozygosity rate of 1.31% and a duplication rate of 1.55% (Fig. 1A).

Fig. 1
figure 1

Feature estimation and assembly of Monochamus alternatus genome. (A) Estimation of M. alternatus genomic features. The 17-mer distributions showed double peaks: the first peak with a coverage of 100 indicates genome duplication, and the highest peak with a coverage of 200 represents a genome-size peak. M. alternatus genome size was calculated to be 667 Mb with heterozygosity rate of 1.31% and duplication rate of 1.55%. (B) Genome-wide contact matrix of Monochamus alternatus generated using Hi-C data. Each black square represents a pseudo-chromosome. The color bar indicates the interaction intensity of Hi-C contacts.

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Genome assembly

A draft genome at contig level was assembled using NextDenovo version 1.2.5 (https://github.com/Nextomics/NextDenovo) with default parameters (genome-size = 667, read-cutoff = 3k) based on Nanopore long reads. Purge_dups was used to remove alternative haplotype and redundant fragments in the contig assembly. We performed Hi-C analysis to further anchor the assembly into chromosome-scale linkage groups. The Hi-C clean reads were cleaned using Fastp22 and mapped to the contigs using BWA. YaHS version 1.2a.123 and Juicertools version 1.19.0224 were used to assemble and manual correction. As a result, 98.21% of the contigs were anchored to 10 pseudo-chromosomes, which were presented in the heatmap of the chromatin contact matrix (Fig. 1B). At last, two rounds of polishing with ONT reads and Illumina reads were performed using NextPolish version 1.4.025. The output chromosome-level genome has a size of 767.12 Mb, N50 of 82.0 Mb, maximum length of 149.24 Mb, and GC content of 32.35% (Table 2).

Table 2 Statistics for the chromosomal-level genome of the Monochamus alternatus.
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Genome annotation

The protein-coding genes in the M. alternatus genome were predicted under three lines of evidence, including RNA-based, ab initio, and homology-based methods. For the RNA-based method, short transcriptome reads were mapped to the genome using Hisat226. Then, the aligned BAM files were used to assemble the transcripts using Stringtie version 2.1.427. The genes were predicted using PASA version 2.0.2 with default settings28. The ab initio prediction was performed using Augustus version 3.4.029 and SNAP version 2006-07-2830. The gene models in Augustus and SNAP were trained based on transcripts longer than 300 bp generated by PASA. In the homology-based prediction, we gathered evidence of homologous genes from Coleoptera species, including Anoplophora glabripennis31, Tribolium castaneum32, Dendroctonus ponderosae33 and Diabrotica virgifera34. Redundant genes in the pooled gene set were removed using CD-HIT35. Maker version 3.01.0436 pipeline was used to perform the homology-based prediction. At last, the evidence from these methods was combined using EvidenceModeler (EVM) version 1.1.137 to obtain a non-redundant consensus official gene set (OGS).

The predicted genes were functionally annotated using Eggnog-Mapper version 2.1.938. Five methods were used to search against several public databases, including Gene Ontology (GO), Clusters of Orthologous Groups of Proteins (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), CAZY, and Pfam. In summary, we identified 16,284 protein-coding genes (Table 2), of which 11,244 were functionally annotated (Table 3).

Table 3 Number of functionally annotated protein-coding gene in different databases.
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Repeats prediction

Homology-based and de novo prediction methods were used to detect transposable elements (TEs). Briefly, repeats sequences were detected using RepeatMasker version 4.1.2 (-no_is -norna -xsmall -q)39, against the Repbase, Dfam database, and species-specific repeat library identified by RepeatModeler version 2.0.3. Finally, 63.95% of the genome was identified to be repeat DNA. Overall, 576,182 transposable elements (TEs), including 178,967 retroelements (189 short interspersed nuclear elements (SINEs), 144,289 long interspersed nuclear elements (LINEs), and 34,489 long terminal repeats (LTR)) and 397,215 DNA transposons were identified. Five hundred twenty-three satellites and 678 simple repeats were identified as tandem repeats (TRs), accounting for 0.03% of the M. alternatus genome (Table 4).

Table 4 Repeats elements statistics in genome of Monochamus alternatus using RepeatMasker.
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Non-coding RNA annotation

For non-coding RNA annotation, the transfer RNA (tRNA) was annotated by tRNAscan-SE version 1.3.1 based on the structural characteristics of tRNA40, whereas the ribosome RNA (rRNA) was predicted by RNAmmer version 1.241,42. We obtained 498 tRNA and 107 rRNA genes, including 98 8s_rRNA, five 28s_rRNA, and four 18s_rRNA genes in the M. alternatus genome (Table 5).

Table 5 Statistics of non-coding RNAs in genomes of Monochamus alternatus.
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Data Records

The genome project was deposited at NCBI under BioProject number PRJNA819115. Illumina sequencing data for genome survey were deposited in the Sequence Read Archive at NCBI under accession number SRR2611552343. Hi-C sequencing data were deposited in the Sequence Read Archive at NCBI under accession number SRR2614633844. Nanopore sequencing raw data were deposited in the Sequence Read Archive at NCBI under accession number SRR2615769845. RNA-seq data were deposited in the Sequence Read Archive at NCBI under accession numbers SRR26116071- SRR2611607346,47,48. The final chromosome assembly, genome structure annotation, amino acid sequences and functional annotation results of protein-coding genes were deposited to Figshare repository under a DOI number of https://doi.org/10.6084/m9.figshare.c.6849162.v149. The final chromosome assembly was deposited in GenBank under accession number JAYMDT00000000050.

Technical Validation

The Hi-C heatmap exhibits the accuracy of genome assembly, with relatively independent Hi-C signals observed between the ten pseudo-chromosomes (Fig. 1B). We assessed the accuracy of the final genome assembly by mapping Illumina short reads to the M. alternatus genome with BWA-MEM2 version 0.7.172151. The mapping rate for Illumina reads was 98.71%. The findings indicate that the quality of our assembled genome is high.

To assess the completeness of genome assembly and OGS, we run Benchmarking Universal Single-Copy Orthologues (BUSCO version 5.2.2) using the insecta_odb10 database, which contains 1367 conserved genes52. For Contig-level, in the first round, the BUSCO analysis showed that 93.8% (single-copied gene: 93.2%, duplicated gene: 0.6%) of 1367 single-copy genes were identified as complete, 3.3% of genes were fragmented, and 2.9% of genes were missing in the assembled genome. For the chromosome-level assembly, BUSCO analysis showed that 99.7% (single-copied gene: 99.0%, duplicated gene: 0.7%) of 1367 genes were identified as complete, 0% of genes were fragmented, while 0.3% of genes were missing in the assembled genome. For OGS, BUSCO analysis showed 96.7% completeness, with only 0.5% of genes duplicated, 1.5% fragmented, and 1.8% missing (Table 6).

Table 6 BUSCO evaluation of genome assemblies.
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