The genome sequence of the blue-tailed damselfly, Ischnura elegans (Vander Linden, 1820)

We present a genome assembly from an individual female Ischnura elegans (the blue-tailed damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence is 1,723 megabases in span. The majority of the assembly (99.55%) is scaffolded into 14 chromosomal pseudomolecules, with the X sex chromosome assembled.


Background
Ischnura elegans, commonly known as the blue-tailed damselfly or common bluetail, is one of the commonest damselflies in the UK, occurring at all latitudes up to the north coast of Scotland. This species is an early coloniser of new habitats and can tolerate moderately polluted water. Larvae may be found among aquatic plants in ponds, lakes, ditches, canals and slow-flowing rivers. In most of England the species is univoltine, with a life cycle completed in one year; however, in northern latitudes and likely over much of Scotland the species is semivoltine, with a life cycle completed in two years.
Males appear dark due to their metallic black abdomen, with a bright blue segment 8 and a green or blue thorax. Females have five different colour morphs: (i) violet (violacea) which mature to be either (ii) olive-green with a brown abdomen spot (infuscans), or (iii) a blue male mimic (typica); or alternatively (iv) orange-pink with a blue abdomen spot (rufescens) which mature to be (v) brown (rufescens-obsoleta) (Brooks & Cham, 2020).
These different morphs likely have a function in mate choice, avoidance of mating harassment and camouflage. Physico-chemical analysis has shown that their coloration is mainly due to a combination of pigments and nanospheres, and that changes in the pigment composition and the packing of the nanospheres during maturation modify their colour (Henze et al., 2019). Both sexes and the different female colour morphs show differential gene expression, with the gene expression of the male mimic morph (typica) being closest to that of the male (Chauhan et al., 2016). Within females, the gene expression between morphs becomes increasingly differentiated during sexual maturation (Willink et al., 2020).
We note the recent release of a genome assembly and annotation for I. elegans by Chauhan et al. (2021). We hope that the high-quality genome assembly described herein, generated as part of the Darwin Tree of Life project, will add to this existing resource and further aid understanding of the biology, physiology and ecology of this species.

Genome sequence report
The genome was sequenced from one female I. elegans collected from Iremonger pond, Nottingham, UK (latitude 52.9354, longitude -1.1544). A total of 26-fold coverage in Pacific Biosciences single-molecule long reads and 64-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 183 missing/misjoins and removed 25 haplotypic duplications, reducing the assembly size by 1.08% and scaffold number by 56.18% and increasing the scaffold N50 by 43.82%.
The final assembly has a total length of 1,723 Mb in 110 sequence scaffolds with a scaffold N50 of 123.6 Mb ( Table 1). The majority of the assembly sequence (99.55%) was assigned to 14 chromosomal-level scaffolds, representing 13 autosomes (numbered by sequence length), and the X sex chromosome (Figure 1-Figure 4; Table 2). The assembly has a BUSCO v5.1.2 (Manni et al., 2021) completeness of 97.2% (single 96.4%, duplicated 0.8%) using the insecta_odb10 reference set (n=1,367). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.   DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute. The ioIscEleg1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Whole organism tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. Low molecular weight DNA was removed from a 200-ng aliquot of extracted DNA using 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing. HMW DNA was sheared into an average fragment size between 12-20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics Chromium read cloud sequencing libraries were constructed according to the manufacturers' instructions. Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (10X) instruments. Hi-C data were generated from remaining tissue using the Arima Hi-C+ kit and sequenced on an Illumina HiSeq X instrument.   or blue thorax. Females have five different colour morphs: (i) immature violet (violacea) thorax with a brown abdomen spot which mature to be (ii) olive-green with (infuscans), or violet thorax with a blue abdomen spot which mature to be (iii) a blue male mimic (androchrome); or alternatively (iv) immature orange-pink thorax with a blue abdomen spot which mature to be (v) ( rufescens-obsoleta) with brown thorax and a brown abdomen spot.