Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)

Abstract

Background The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings. Findings We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution. Conclusions The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.

A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly

“…We then mapped these proteins to the chromosome level assembly using miniprot v0.4 ( Li 2022 ) and re-trained Augustus ( Stanke et al 2008 , 2006 ) using the scaffold-level coding sequences, with 1000 base pairs surrounding each sequence as the training set. As this annotation resulted in a high number of genes, and a less-than ideal BUSCO score we also mapped the protein set of Pantala flavescens ( Liu et al 2022 ) to the masked chromosome level assembly using miniprot v0.4( Li 2022 ), and extracted the mapped Pantala proteins, the protein set from the augustus annotation, and the protein set of the mapped proteins from their respective gff files with gffread ( Pertea 2022 ). We combined all three protein sets and clustered the proteins at 80* similarity with CD-HIT v4.8.1 ( Fu et al 2012 ).…”

A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly

“…We then mapped these proteins to the chromosome level assembly using miniprot v0.4 (Li 2022) and re-trained Augustus (Stanke et al 2008, 2006) using the scaffold-level coding sequences, with 1000 base pairs surrounding each sequence as the training set. As this annotation resulted in a high number of genes, and a less-than ideal BUSCO score we also mapped the protein set of Pantala flavescens (Liu et al 2022) to the masked chromosome level assembly using miniprot v0.4(Li 2022), and extracted the mapped Pantala proteins, the protein set from the augustus annotation, and the protein set of the mapped proteins from their respective gff files with gffread (Pertea 2022). We combined all three protein sets and clustered the proteins at 80* similarity with CD-HIT v4.8.1 (Fu et al 2012).…”

High levels of chromosomal synteny in 250 million year old groups of dragonflies and damselflies (Insecta:Odonata)

“…To determine the amount of conserved synteny across Odonata we used the chromosome level genome assemblies of the Zygoptera Platycnemis pennipes (downloaded from NCBI) and Ischnura elegans 21 and the Anisoptera Pantala avescens 20 and Tanypteryx hageni 19 . All genomes have been shown to be of relatively high quality 19 , and all but P. pennipes have been annotated.…”

“…As with many other taxa, the advent of long-read sequencing has resulted in a growing number of publicly available genome assemblies from the order Odonata. There are now four chromosome length assemblies for Odonata: that of: the black petaltail 19 (Tanypyeryx hageni) and wandering glider 20 (Pantala avescens) dragon ies, and the blue-tailed 21 (Ischnura elegans) and white-legged (Platycnemis pennipes) damsel ies. Serendipitously, Platycnemis pennipes has retained the putative ancestral karyotype (2n = 25), while Pantala avescens (2n = 23) and Tanypteryx hageni (2n = 17) have a reduced karyotype, and Ischnura elegans (2n = 27) has expanded upon the ancestral karyotype 16 .…”