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Data Note

The complete genome sequences of 22 parrot species (Psittaciformes, Aves)

[version 1; peer review: 3 approved with reservations]
PUBLISHED 12 Nov 2020
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This article is included in the Genomics and Genetics gateway.

Abstract

The parrots (Psittaciformes, Aves) are a group of colorful, intelligent, long-lived birds with a wide range of body sizes and plumage colors and patterns.  One third of the parrot species is threatened with extinction due to habitat loss and the pet trade, a larger percentage than any other comparable bird order.  We present the complete genome sequences of 22 species of parrots from 14 genera and 3 families: Anodorhynchus hyacinthinus, Ara ararauna, Ara chloropterus, Ara glaucogularis, Ara militaris, Aratinga solstitialis, Aratinga weddellii, Cacatua leadbeateri, Eclectus roratus, Eupsittula pertinax, Guaruba guarouba, Lorius garrulus, Myiopsitta monachus, Nymphicus hollandicus, Pionus senilis, Psittacus erithacus, Psittacus timneh, Psitteuteles goldiei, Pyrrhura frontalis, Pyrrhura griseipectus, Pyrrhura molinae, Pyrrhura perlata.  Genomic data can be used to better understand species identity, hybridization, genetic diversity, and identification of animal products possibly derived from endangered species.

Keywords

Parrots, birds, Psittaciformes, cockatoos, genomes

Introduction

The parrots (Psittaciformes, Aves) are an order of 370 extant species (Clements et al., 2019) characterized by high intelligence (Pepperberg, 2017), diverse plumage colors and patterns (Berg & Bennett, 2010), and clawed zygodactyl feet (Botelho et al., 2014). A third of all parrot species are threatened by extinction due to habitat loss and the practice of capturing young birds for the pet trade (Butchart et al., 2004).

Complete genome sequences for parrot species will benefit such diverse fields as biodiversity, evolutionary studies, species hybridization, and research into the development of brain function. Genomic data will also aid in the development of molecular markers to identify products, which may be derived from endangered species (Yang et al., 2018).

Methods

Samples from 22 parrot species were obtained from molted feathers from pet birds, and blood samples from birds from captive breeding programs (Table 1). Where blood samples were used, they were obtained by a licensed veterinarian coinciding with a standard health check. Animals were handled in a manner consistent with accepted practices (NRC, 2011). In the case of molted feathers, pulp was excised from the shaft of a large tail or primary wing feather prior to extraction.

Table 1. Species sequenced for this study.

Scientific nameCommon nameAccession numberGenome sizeSample typeFamily name
Anodorhynchus
hyacinthinus
Hyacinth MacawGCA_0099364451,119,461,287featherPsittacidae
Ara ararauna Blue-And-Yellow
Macaw
GCA_0100148051,128,178,780bloodPsittacidae
Ara chloropterus Red-And-Green
Macaw
GCA_0100147251,117,846,189featherPsittacidae
Ara glaucogularis Blue-Throated MacawGCA_0100154251,135,105,966featherPsittacidae
Ara militaris Military MacawGCA_0100159651,177,230,593featherPsittacidae
Aratinga solstitialis Sun ParakeetGCA_0098671951,214,690,015featherPsittacidae
Aratinga weddelliiDusky-headed
Parakeet
GCA_0098672051,114,053,963bloodPsittacidae
Cacatua leadbeateri Major Mitchell's
Cockatoo
GCA_0100150451,069,984,771featherCacatuidae
Eclectus roratus Eclectus ParrotGCA_0117635351,101,365,900featherPsittacidae
Eupsittula pertinax Brown-Throated
Parakeet
GCA_0113171851,171,654,275featherPsittacidae
Guaruba guaroubaGolden ParakeetGCA_0118000951,151,548,123bloodPsittacidae
Lorius garrulus Chattering LoryGCA_0100149251,091,728,784featherPsittaculidae
Myiopsitta monachus Monk ParakeetGCA_0130360051,118,816,385featherPsittacidae
Nymphicus hollandicus CockatielGCA_0098234351,205,077,083featherCacatuidae
Pionus senilis White-Capped ParrotGCA_0117627251,067,577,099featherPsittacidae
Psittacus erithacus Grey ParrotGCA_0098672351,118,034,822bloodPsittacidae
Psittacus timnehTimneh ParrotGCA_0098673151,103,923,287bloodPsittacidae
Psitteuteles goldieiGoldie's LorikeetGCA_0100148751,125,670,205featherPsittaculidae
Pyrrhura frontalis Maroon-Bellied
Parakeet
GCA_0100148651,112,821,352bloodPsittacidae
Pyrrhura griseipectus Gray-Breasted
Parakeet
GCA_0100149651,129,186,538bloodPsittacidae
Pyrrhura molinae Green-Cheeked
Parakeet
GCA_0117633551,122,251,672bloodPsittacidae
Pyrrhura perlataCrimson-bellied
Parakeet
GCA_0117634551,111,465,322bloodPsittacidae

DNA extraction was performed on blood and feather pulp using the Qiagen DNAeasy genomic extraction kit, using the manufacturer’s process. A paired-end sequencing library was constructed using the Illumina TruSeq kit, according to the manufacturer’s instructions. The library was commercially sequenced at Genewiz (New Jersey, USA) on an Illumina Hi-Seq platform in paired-end, 2 × 150bp format.

The resulting fastq files were trimmed of adapter/primer sequence and low-quality regions with Trimmomatic (v0.33) (Bolger et al., 2014). The trimmed sequence was assembled by SPAdes (v2.5) (Bankevich et al., 2012). This was followed by a finishing step using RagTag (v1.0.0) (Alonge, 2020) to make additional contig joins based on conserved regions in other parrot species: Melopsittacus undulatus (GCA_012275295), Amazona guildingii (GCA_013399615), Agapornis roseicollis (GCA_002631895), and other species in this study.

Results

The genome sizes and NCBI Assembly accessions for each species are shown in Table 1.

Genome sizes ranged from 1.07 – 1.21 G (scaffolded), with no clear delineation between the three represented families (Psittacidae, Psittaculidae, Cacatuidae).

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Hains T, O'Neill K, Velez J et al. The complete genome sequences of 22 parrot species (Psittaciformes, Aves) [version 1; peer review: 3 approved with reservations]. F1000Research 2020, 9:1318 (https://doi.org/10.12688/f1000research.25560.1)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Open Peer Review

Current Reviewer Status: ?
Key to Reviewer Statuses VIEW
ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 1
VERSION 1
PUBLISHED 12 Nov 2020
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Reviewer Report 26 Oct 2021
Roberto Ambrosini, Department of Environmental Science and Policy, University of Milan, via Celoria 26, Milano, 20133, Italy 
Simona Secomandi, Department of Biosciences, University of Milan, via Celoria 26, Milano, 20133, Italy 
Approved with Reservations
VIEWS 10
The paper by Hains and co-authors provides NCBI accession numbers for 22 scaffold-level parrot genome assemblies. These data have the potential to add a consistent number of parrot genomes to the current literature and are therefore very valuable. However, there ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Ambrosini R and Secomandi S. Reviewer Report For: The complete genome sequences of 22 parrot species (Psittaciformes, Aves) [version 1; peer review: 3 approved with reservations]. F1000Research 2020, 9:1318 (https://doi.org/10.5256/f1000research.28208.r96540)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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23
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Reviewer Report 08 Apr 2021
Devon DeRaad, Department of Ecology & Evolutionary Biology, Kansas University, Kansas, USA 
John McCormack, Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA 
Approved with Reservations
VIEWS 23
These are potentially very valuable data for avian genomics, as they increase the number of parrot genomes many times. These data will provide valuable resources for evolution and conservation genomics study.

This study has a few limitations, ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
DeRaad D and McCormack J. Reviewer Report For: The complete genome sequences of 22 parrot species (Psittaciformes, Aves) [version 1; peer review: 3 approved with reservations]. F1000Research 2020, 9:1318 (https://doi.org/10.5256/f1000research.28208.r82331)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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29
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Reviewer Report 19 Feb 2021
Paweł Mackiewicz, Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland 
Approved with Reservations
VIEWS 29
The manuscript was submitted to the section Data Note. It presents very briefly the description of nuclear genomes from 22 parrot species. Although the importance of these genomes is crucial for various analyses, the presentation should be improved.
The title indicates that ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Mackiewicz P. Reviewer Report For: The complete genome sequences of 22 parrot species (Psittaciformes, Aves) [version 1; peer review: 3 approved with reservations]. F1000Research 2020, 9:1318 (https://doi.org/10.5256/f1000research.28208.r77387)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.

Comments on this article Comments (0)

Version 1
VERSION 1 PUBLISHED 12 Nov 2020
Comment
Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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