Abstract
We present genomes and pupal transcriptomes of the Mediterranean flour moth, Ephestia kuehniella. The moth is a world-wide storage pest as well as a laboratory species with a considerable background in developmental biology, genetics, and cytogenetics. The sequence data were derived from a highly inbred laboratory strain and, hence, display very little heterozygosity. Female and male genomes and transcriptomes are represented separately in two sets each of raw and assembled sequence data. They are designed as a basis to develop new strategies in pest control, to elucidate the molecular adaptation for its peculiar lifestyle, and for research on sex chromosome structure, sex determination and sex-specific gene activity. For a test, all genes known or suspected to have a role in sex determination were extracted from the data. Raw sequencing data and assemblies are available at European Nucleotide Archive under accession number PRJEB49052.
Keywords: Female and male genomes, Female and male transcriptomes, Lepidoptera, de novo assembly, Heterozygosity
Specifications Table
| Subject | Entomology and insect science |
| Specific subject area | Insects, Lepidoptera, Genomics, Transcriptomics |
| Type of data | Raw data from DNA and RNA-sequencing of females and males (fastq files) Genome assembly (fasta files) Transcriptome assembly (fasta files) Table with ENA accession numbers and Genbank IDs Table showing summary statistics of the assemblies |
| How the data were acquired | Illumina HiSeq 2500 sequencing platform, paired-end sequencing data for DNA and RNA, mate pairs with 8 kb insert size for DNA |
| Data format | Raw data Analyzed data |
| Parameters of data collection | Data collection contains raw genome and transcriptome data for two different datasets (referred to as Mainz and Novogene) of the laboratory strain L of E. kuehniella. Additionally, transcriptome assemblies of both datasets and a genome assembly of the dataset Mainz are available. |
| Description of data collection | Total RNA and total DNA from females and males was extracted from mid-stage pupae of laboratory strain L of E. kuehniella (Mainz: one female and one male each; dataset Novogene: 5 females and 5 males each and pooled by sex) and subjected to HiSeq Illumina paired-end (Mainz: 2 × 250 bp; Novogene: 2 × 150 bp) and mate-pair (Mainz only, 8 kb insert size, 2 × 250 bp) sequencing. |
| Data source location |
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| Data accessibility | The raw sequence reads, and the assemblies can be obtained through ENA study accession number PRJEB49052. Gene sequences for sex determining genes were submitted to Genbank. Repository name: European Nucleotide Archive (ENA) Data identification number: PRJEB49052 Direct URL to data: https://www.ebi.ac.uk/ena/browser/view/PRJEB49052 |
Value of the Data
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The source of the genomes and transcriptomes, E. kuehniella, is a storage pest with world-wide distribution. It is also a favorable laboratory species and has a rich background in developmental biology, genetics, and cytogenetics.
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Researchers developing new molecular strategies of pest control will benefit from the data as well as those interested in insect phylogeny, genetic adaptation for the peculiar lifestyle of the species and its sex determination, sex chromosome content and sex-specific expression of genes.
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The female and male genomes and transcriptomes are from a highly inbred line and have a very low level of heterozygosity. This makes them especially valuable for female-versus-male comparisons. The developmental stage, mid-pupa, is a stage when genes involved in morphogenesis and sex-differentiation are supposed to be active.
1. Data Description
The dataset contains a draft genome and draft pupal transcriptome assembly, separately from females and males of the Mediterranean flour moth, E. kuehniella (Lepidoptera, Pyralidae), besides two sets of raw sequencing data referred to as ‘Mainz’ and ‘Novogene’. For dataset ‘Mainz’, data from a highly inbred line was collected from a single female and a single male individual for the transcriptome assembly and from two female and two male individuals for the genome assembly. RNA libraries were submitted to paired-end Illumina sequencing and DNA libraries were sequenced using paired-end and 8 kb mate-pair Illumina sequencing technology (dataset ‘Mainz’). The raw sequencing data and the assemblies can be obtained from ENA study accession number PRJEB49052 (accession numbers for genome assemblies derived from the ‘Mainz’ dataset: female ERS8464940, male ERS8464941; accession numbers for transcriptome assemblies: female ERS8464942, male ERS8464943; more details are given in Table 1). A second set of raw data (dataset ‘Novogene’) was obtained by pooling 5 females and 5 males separately of the same inbred E. kuehniella strain and can be obtained from the same study accession number. RNA and DNA libraries from this dataset were sequenced using paired-end sequencing and the RNA-seq data was used to perform a second transcriptome assembly for each sex (accession numbers for transcriptome assemblies derived from the ‘Novogene’ dataset: female ERS8464945, male ERS8464946).
Table 1.
Accession numbers for the European Nucleotide Archive (ENA) for the sequencing data and Genbank IDs for E. kuehniella orthologs genes known or suspected to have a role in its sex determination.
| Repository | ID | Dataset |
|---|---|---|
| ENA | ERS8464763 | Female genome Mainz raw data |
| ERS8464764 | Female transcriptome Mainz raw data | |
| ERS8464765 | Female genome Mainz raw data (8 kb mate pairs) | |
| ERS8464766 | Male genome Mainz raw data | |
| ERS8464767 | Male transcriptome Mainz raw data | |
| ERS8464768 | Male genome Mainz raw data (8 kb mate pairs) | |
| ERS8464769 | Female genome Novogene raw data | |
| ERS8464770 | Female genome Novogene raw data | |
| ERS8464771 | Female transcriptome Novogene raw data | |
| ERS8464772 | Male genome Novogene raw data | |
| ERS8464773 | Male genome Novogene raw data | |
| ERS8464774 | Female transcriptome Novogene raw data | |
| ERS8464940 | Female genome assembly Mainz | |
| ERS8464941 | Male genome assembly Mainz | |
| ERS8464942 | Female transcriptome assembly Mainz | |
| ERS8464943 | Male transcriptome assembly Mainz | |
| ERS8464944 | Combined female/male transcriptome assembly Novogene | |
| ERS8464945 | Female transcriptome assembly Novogene | |
| ERS8464946 | Male transcriptome assembly Novogene | |
| Genbank | OU228360 | E. kuehniella mRNA for Ekdsx f1 (female splice variant 1) |
| OU228361 | E. kuehniella mRNA for Ekdsx f2 (female splice variant 2) | |
| OU228362 | E. kuehniella mRNA for Ekdsx m1(male splice variant 1) | |
| OU228363 | E. kuehniella mRNA for fruitless (Ekfruitless) | |
| OU228364 | E. kuehniella mRNA for heatshock protein 70 (EkHSP70) | |
| OU228365 | E. kuehniella mRNA for IGF-II mRNA binding protein (EkIMP) | |
| OU228366 | E. kuehniella mRNA for P-element somatic inhibitor (EkPSI) | |
| OU228367 | E. kuehniella mRNA for Sex lethal (EkSxl) | |
| OU228368 | E. kuehniella mRNA for transformer-2 (EkTra2) | |
Genome sizes for the haploid female and male genomes were estimated using the ‘Novogene’ data. Estimates based on a kmer approach were 363Mb (megabases) for the haploid female genome and 365Mb for the male genome. This is significantly less than 440Mb, the value determined by flow cytometry and confirmed by Feulgen cytometry [1]. Assembled genomes were 357Mb (female) and 354Mb (male) with an N50 of 11,860 bp (female) and 12,636 bp (male). The longest contigs were ∼197 kb in the female genome assembly and ∼426 kb in the male assembly, respectively. GC content was very similar between the two sexes (∼36%). Further assembly details are shown in Table 2. The completeness of the genome and transcriptome assemblies was assessed using BUSCO with the lepidoptera-odb10 lineage dataset (Table 2). The ‘Novogene’ dataset was used to estimate heterozygosity. As expected from a highly inbred line, heterozygosity was very low. For the female genome, heterozygosity was estimated between 0.152 and 0.156% and for the male assembly the estimated heterozygosity was between 0.034 and 0.037%. The higher estimate of heterozygosity in females is probably due to the fact that females are the heterogametic sex in E. kuehniella and have WZ sex chromosomes while males are homogametic with a ZZ sex chromosome pair.
Table 2.
Assembly statistics for the genome and transcriptome assembly and results from benchmarking universal single-copy orthologs (BUSCO) analysis against lepidoptera-odb10 as reference dataset for genome and transcriptome completeness. Percentage of genes per assembly from BUSCO analysis are shown for complete single copy and duplicated genes as well as for fragmented genes (5286 genes in total).
| Genome Mainz |
Transcriptome Mainz |
Transcriptome Novogene |
|||||
|---|---|---|---|---|---|---|---|
| Features | Female | Male | Female | Male | Female | Male | |
| Assembly | Size (bp) | 357,446,945 | 353,955,619 | 61,075,989 | 68,091,461 | 144,998,424 | 157,359,019 |
| Sequences | 90,999 | 90,445 | 87,516 | 101,822 | 141,949 | 150,130 | |
| N50 (bp) | 11,860 | 12,636 | 10,905 | 13,268 | 2271 | 2335 | |
| L50 | 7830 | 7172 | 1253 | 1127 | 16,542 | 17,474 | |
| N90 (bp) | 1662 | 1636 | 268 | 264 | 355 | 364 | |
| L90 | 41,028 | 39,236 | 61,107 | 72,169 | 88,955 | 93,588 | |
| Longest contig (bp) | 197,352 | 425,840 | 24,754 | 36,418 | 49,425 | 49,499 | |
| Gaps (runs of Ns) | 34,083 | 25,950 | 2581 | 2965 | 0 | 0 | |
| Number N | 31,356,943 | 30,452,154 | 22,651 | 26,965 | 0 | 0 | |
| GC (%) | 35.97 | 35.96 | 38.43 | 38.07 | 41.27 | 41.11 | |
| BUSCO | Complete | 4352 | 4477 | 3998 | 3972 | 4790 | 4956 |
| Complete: single copy | 4313 (81.6%) | 4440 (84.0%) | 3961 (74.9%) | 3923 (74.2%) | 2875 (54.4%) | 2872 (54.3%) | |
| Complete: duplicated | 39 (0.7%) | 37 (0.7%) | 37 (0.7%) | 49 (0.9%) | 1915 (36.2%) | 2084 (39.4%) | |
| Fragmented | 528 (10.0%) | 430 (8.1%) | 406 (7.7%) | 409 (7.7%) | 79 (1.5%) | 52 (1.0%) | |
| Missing | 406 (7.7%) | 379 (7.2%) | 882 (16.7%) | 905 (17.1%) | 417 (7.9%) | 278 (5.3%) | |
For a test of the data set, we searched for the E. kuehniella orthologs of all genes known or suspected to have a role in its sex determination. EkMasc and EkMascB, the orthologues of Masculinizer (Masc) from Bombyx mori were recently described to produce the primary signal of the sex determining cascade in E. kuehniella [2]. Our assemblies allowed us to extract these and Ekdsx, EkPSI, EkIMP, EkTra2, EkSxl, EkHSP70, as well as the sex-specific splice variants of Ekdsx (GenBank accession numbers: OU228360–OU228368; see Table 1 for details).
2. Experimental Design, Materials and Methods
2.1. Sample collection
E. kuehniella strain L has been kept in laboratory cultures for more than 80 years. For sequencing, female and male mid-stage pupae were selected. One female and one male pupa each were used in paired-end and 8 kb mate-pair genome sequencing as well as in paired end transcriptome sequencing for data set 'Mainz'. The ‘Novogene’ data set was derived from mid-stage pupae for RNA and DNA sequencing (five females and males each, which were pooled by sex for sequencing).
2.2. Library preparation and sequencing
For data set `Mainz', DNA and RNA extraction and sequencing was performed by StarSeq (Mainz, Germany) and for the 'Novogene' by Novogene (Hongkong, China). Short-read libraries were prepared using the TruSeq Library Preparation Kit, and sequencing was performed using the Illumina HiSeq 2500 system. For dataset ‘Mainz’ sequences were labeled with barcodes (female: paired-end genome CGAGGCTG/CAGCCTCG, paired-end transcriptome TCCGCGAA/TTCGCGGA, mate-pairs ACAGTGAT; male: paired-end genome CGTACTAG, paired-end transcriptome TCTCGCGC, mate-pairs GCCAATAT). For dataset ‘Novogene’ the barcodes were removed by Novogene. Libraries from ‘Mainz’ were sequenced using 2 × 250 bp reads and ‘Novogene’ was sequenced using 2 × 150 bp.
2.3. Genome and transcriptome assembly
Raw sequencing reads from dataset ‘Mainz’ were quality checked and adaptor sequences were removed. For both sexes, a de novo genome assembly was performed using CLC Assembly Cell v4.0 (QIAGEN Digital Insights, Redwood City, USA) applying a deBruijn graph model (parameter settings: bubblesize = 300, kdef which refers to default kmer size). Transcriptome assemblies for dataset `Novogene' were performed using Trinity [3] (v2.8.4) with the following command line:
Trinity –seqType fq –max_memory 180 G –left FORWARD.fastq –right BACKWARD.fastq –CPU 24 –trimmomatic –jaccard_clip –full_cleanup –output assembly_output
Quality assessment of genome and transcriptome assemblies was done applying BUSCO [4] (v4.0.4) using the lepidoptera-odb10 lineage dataset (creation date 2020–08–05) with no additional third-party components.
2.4. Data analysis
Genome size, and heterozygosity were estimated using a kmer-based approach as implemented in jellyfish [5] (kmer size 27) and resulting histograms were uploaded to GenomeScope [6] (http://qb.cshl.edu/genomescope) to perform the analysis.
CRediT authorship contribution statement
Axel Künstner: Data curation, Investigation, Writing – original draft, Writing – review & editing. Hauke Busch: Writing – review & editing. Enno Hartmann: Writing – review & editing. Walther Traut: Conceptualization, Resources, Investigation, Data curation, Writing – original draft, Writing – review & editing.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgments
We thank the computational support from the OMICS compute cluster at the University of Lübeck. This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy—EXC 22167–390884018 to H.B.
Data Availability
Sequencing read data and assemblies for Ephestia kuehniella draft genomes and transcriptomes (Original data) (European Nucleotide Archive (ENA)).
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Associated Data
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Data Availability Statement
Sequencing read data and assemblies for Ephestia kuehniella draft genomes and transcriptomes (Original data) (European Nucleotide Archive (ENA)).