The Complete Genome Sequences of 94 Species of Parrots (Psittaciformes, Aves)

Introduction

Parrots (Psittaciformes) include 401 extant species in 92 genera (Lepage, Vaidya, and Guralnick 2014). Found primarily in tropical and subtropical regions, the highest biodiversity of parrots is found in South America and Australasia. Parrots are among the most intelligent of birds. The ability of some species to imitate human speech, and their colorful plumage has made them popular in the pet trade. The capturing of young parrots for sale as pets, along with habitat loss, has greatly diminished the wild populations of some species. The IUCN lists approximately a third of parrot species threatened with extinction.

We present the assembled genome sequences from 94 extant species of parrots. Tissue samples were obtained from live birds, preserved birds, and tissue samples from museums. More detailed information about the specimen used for each species can be found in the Biosample linked to each genome assembly in Genbank.

Methods

DNA extraction was performed using the Qiagen DNAeasy genomic extraction kit using the standard process. A paired-end sequencing library was constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150 bp format. The resulting fastq files were trimmed of adapter/primer sequence and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v2.5 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).

Results and Data Availability

All data, including raw reads and assembled genome sequence, is available via Genbank.

Funding

Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.