Describing biodiversity in the genomics era: Description of a new species of Nearctic Cynipidae gall wasp and its genome

Gall wasps (Hymenoptera: Cynipidae) specializing on live oaks in the genus Quercus (subsection Virentes) are a relatively diverse and well-studied community with 14 species described to date, albeit with incomplete information on their biology, life history, and genetic structure. Incorporating an integrative taxonomic approach, we combine morphology, phenology, behavior, genetics, and genomics to describe a new species, Neuroterus valhalla sp. nov. The alternating generations of this species induce galls on the catkins and stem nodes of Quercus virginiana and Q. geminata in the southern United States. We describe both generations in the species’ life cycle, and primarily use samples from a population in the center of Houston, Texas, thus serving as an example of the undescribed biodiversity still present in well-traveled urban centers. In parallel, we present a draft assembly of the N. valhalla genome providing a direct link between the type specimen and reference genome. The genome of..., GENOME SEQUENCING, ASSEMBLY AND ANNOTATION

To sequence N. valhalla’s genome, we extracted whole genomic DNA from a single female from the catkin generation using the DNeasy Blood and Tissue Kit (Qiagen, Germany) as described above. A paired-end sequencing library was then constructed with the Illumina TruSeq kit (Illumina, USA) using the standard adapters, and sequencing was performed at Genewiz (New Jersey, USA) on an Illumina X-Ten sequencing platform. Raw data was submitted to Genbank Short Read Archive (Accession number SRX7007139). Then, fastq files were filtered and trimmed by Trimmomatic v.0.39 (Bolger et al., 2014), first removing sliding windows of 5 nucleotides with quality average below 20, followed by a hard-trailing trim of nucleotides with quality below 15. Trimmed reads were then assembled de novo by SPAdes v3.14.0 (Bankevich et al., 2012) using kmer-sizes of 27,37,47,57,67,77,87,97,107,117 and 127. Assembly quality and completeness were accessed by quast v5.0.2 (Gurev..., , # Supplementary data on the \"Describing biodiversity in the genomics era: Description of a new species of Nearctic Cynipidae gall wasp and its genome\"

https://doi.org/10.5061/dryad.zgmsbccc8

Files in this folder include:

**c\_valhalla\_assembly\_v1.fasta**
Fasta file of the Neuroterus valhalla assembly version used in the manuscript.

**EVM\_cvalhalla.all.gff3**
A gff filing containing the gene annotation in the N.valhalla genome. See methods for further details.

**Repeats\_annotation.gff**
A gff file containing the annotation of the repeat sequences in the genome. See methods for further details.

**cvalhalla-families.fa**
A fasta file containing the repeat sequences families from the N. valhalla genome. See methods for further details.

**Neuroterus\_COI.treefile**
Tree file for constructing figure 2 (the genetic barcoding COI phylogeny). See methods and supplementary materials for further details on treebuilding methods and sequences used.

**Neuroterus\_COI**
A Fasta file contai...