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

Taylor Hains; Kathleen O'Neill; Jafet Velez; Nancy Speed; Susan Clubb; Taras Oleksyk; Stacy Pirro

doi:10.12688/f1000research.25560.1

Home Browse The complete genome sequences of 22 parrot species (Psittaciformes,...

ALL Metrics

-

Views

-

Downloads

Get PDF

Get XML

Export

▬

✚

Data Note

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

[version 1; peer review: 3 approved with reservations]

Taylor Hains¹, Kathleen O'Neill², Jafet Velez³, [...] Nancy Speed⁴, Susan Clubb⁴, Taras Oleksyk⁵, Stacy Pirro ²

Taylor Hains¹, Kathleen O'Neill², [...] Jafet Velez³, Nancy Speed⁴, Susan Clubb⁴, Taras Oleksyk⁵, Stacy Pirro ²

PUBLISHED 12 Nov 2020

Author details Author details

¹ Parrot Conservation, Terra Wildlife Genomics, Washington, DC, 20037, UK
² Biodiversity, Iridian Genomes, Bethesda, MD, 20817, USA
³ Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service, Rio Grande, PR, 00745, USA
⁴ Rainforest Clinic for Birds & Exotics, Hurricane Aviaries Inc, Loxahatchee, FL, 33470, USA
⁵ Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA

Taylor Hains
Roles: Resources

Kathleen O'Neill
Roles: Resources

Jafet Velez
Roles: Resources

Nancy Speed
Roles: Resources

Susan Clubb
Roles: Resources

Taras Oleksyk
Roles: Resources

Stacy Pirro
Roles: Funding Acquisition, Investigation, Methodology, Project Administration, Software

OPEN PEER REVIEW

REVIEWER STATUS

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

Corresponding author: Stacy Pirro

Competing interests: No competing interests were disclosed.

Grant information: This work was supported by Iridian Genomes [IRGEN-9223].

Copyright: © 2020 Hains T et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: 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) First published: 12 Nov 2020, 9:1318 (https://doi.org/10.12688/f1000research.25560.1) Latest published: 12 Nov 2020, 9:1318 (https://doi.org/10.12688/f1000research.25560.1)

Editorial note

Editorial note (3rd July 2023): Peer review activity for this article has been discontinued following discussion and agreement between the authors and F1000 Editorial Team. As per our policies on discontinuing peer review, the article is now considered equivalent to a preprint and the authors have chosen to submit the manuscript to a journal for peer review and publication elsewhere.

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 name	Common name	Accession number	Genome size	Sample type	Family name
Anodorhynchus hyacinthinus	Hyacinth Macaw	GCA_009936445	1,119,461,287	feather	Psittacidae
Ara ararauna	Blue-And-Yellow Macaw	GCA_010014805	1,128,178,780	blood	Psittacidae
Ara chloropterus	Red-And-Green Macaw	GCA_010014725	1,117,846,189	feather	Psittacidae
Ara glaucogularis	Blue-Throated Macaw	GCA_010015425	1,135,105,966	feather	Psittacidae
Ara militaris	Military Macaw	GCA_010015965	1,177,230,593	feather	Psittacidae
Aratinga solstitialis	Sun Parakeet	GCA_009867195	1,214,690,015	feather	Psittacidae
Aratinga weddellii	Dusky-headed Parakeet	GCA_009867205	1,114,053,963	blood	Psittacidae
Cacatua leadbeateri	Major Mitchell's Cockatoo	GCA_010015045	1,069,984,771	feather	Cacatuidae
Eclectus roratus	Eclectus Parrot	GCA_011763535	1,101,365,900	feather	Psittacidae
Eupsittula pertinax	Brown-Throated Parakeet	GCA_011317185	1,171,654,275	feather	Psittacidae
Guaruba guarouba	Golden Parakeet	GCA_011800095	1,151,548,123	blood	Psittacidae
Lorius garrulus	Chattering Lory	GCA_010014925	1,091,728,784	feather	Psittaculidae
Myiopsitta monachus	Monk Parakeet	GCA_013036005	1,118,816,385	feather	Psittacidae
Nymphicus hollandicus	Cockatiel	GCA_009823435	1,205,077,083	feather	Cacatuidae
Pionus senilis	White-Capped Parrot	GCA_011762725	1,067,577,099	feather	Psittacidae
Psittacus erithacus	Grey Parrot	GCA_009867235	1,118,034,822	blood	Psittacidae
Psittacus timneh	Timneh Parrot	GCA_009867315	1,103,923,287	blood	Psittacidae
Psitteuteles goldiei	Goldie's Lorikeet	GCA_010014875	1,125,670,205	feather	Psittaculidae
Pyrrhura frontalis	Maroon-Bellied Parakeet	GCA_010014865	1,112,821,352	blood	Psittacidae
Pyrrhura griseipectus	Gray-Breasted Parakeet	GCA_010014965	1,129,186,538	blood	Psittacidae
Pyrrhura molinae	Green-Cheeked Parakeet	GCA_011763355	1,122,251,672	blood	Psittacidae
Pyrrhura perlata	Crimson-bellied Parakeet	GCA_011763455	1,111,465,322	blood	Psittacidae

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).

Data availability

Underlying data

Accession numbers for all genome sequences in GenBank can be found in Table 1.

Faculty Opinions recommended

References

Alonge M: Ragtag: Reference-guided genome assembly correction and scaffolding. GitHub Archive. 2020. Publisher Full Text
Bankevich A, Nurk S, Antipov D, et al.: SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012; 19(5): 455–477. PubMed Abstract | Publisher Full Text | Free Full Text
Berg ML, Bennett ATD: The evolution of plumage colouration in parrots: a review. Emu - Austral Ornithology. 2010; 110(1): 10–20. Publisher Full Text
Bolger AM, Lohse M, Usadel B: Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. 2014; 30(15): 2114–20. PubMed Abstract | Publisher Full Text | Free Full Text
Botelho JF, Smith-Paredes D, Nuñez-Leon D, et al.: The developmental origin of zygodactyl feet and its possible loss in the evolution of Passeriformes. Proc Biol Sci. 2014; 281(1788): 20140765. PubMed Abstract | Publisher Full Text | Free Full Text
Butchart SH, Stattersfield AJ, Bennun LA, et al.: Measuring global trends in the status of biodiversity: red list indices for birds. PLoS Biol. 2004; 2(12): e383. PubMed Abstract | Publisher Full Text | Free Full Text
Clements JF, Schulenberg TS, Iliff MJ, et al.: The eBird/Clements Checklist of Birds of the World: v2019. 2019. Reference Source
National Research Council: Guide for the Care and Use of Laboratory Animals. Eighth edition, 2011. Reference Source
Pepperberg IM: "Birdbrains" should not be ignored in studying the evolution of g. Behav Brain Sci. 2017; 40: e216. PubMed Abstract | Publisher Full Text
Yang F, Ding F, Chen H, et al.: DNA barcoding for the identification and authentication of animal species in traditional medicine. Evid Based Complement Alternat Med. 2018; 2018: 5160254. PubMed Abstract | Publisher Full Text | Free Full Text

Comments on this article Comments (0)

Version 1

VERSION 1 PUBLISHED 12 Nov 2020

Author details Author details

¹ Parrot Conservation, Terra Wildlife Genomics, Washington, DC, 20037, UK
² Biodiversity, Iridian Genomes, Bethesda, MD, 20817, USA
³ Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service, Rio Grande, PR, 00745, USA
⁴ Rainforest Clinic for Birds & Exotics, Hurricane Aviaries Inc, Loxahatchee, FL, 33470, USA
⁵ Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA

Taylor Hains
Roles: Resources

Kathleen O'Neill
Roles: Resources

Jafet Velez
Roles: Resources

Nancy Speed
Roles: Resources

Susan Clubb
Roles: Resources

Taras Oleksyk
Roles: Resources

Stacy Pirro
Roles: Funding Acquisition, Investigation, Methodology, Project Administration, Software

Competing interests

No competing interests were disclosed.

Grant information

This work was supported by Iridian Genomes [IRGEN-9223].

Article Versions (1)

version 1

Published: 12 Nov 2020, 9:1318

https://doi.org/10.12688/f1000research.25560.1

Copyright

© 2020 Hains T et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Download

Export To

metrics

	Views	Downloads
F1000Research	-	-
PubMed Central Data from PMC are received and updated monthly.	-	-

Citations

0

SEE MORE DETAILS

CITE

how to cite this article

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.

track

receive updates on this article

Track an article to receive email alerts on any updates to this article.

Open Peer Review

Current Reviewer Status: ?

Key to Reviewer Statuses VIEW HIDE

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

Views

10

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

https://doi.org/10.5256/f1000research.28208.r96540

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

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 are a series of points that we think can be improved.

Despite this work being published as a data note and no detailed results are therefore expected, the data description is too brief, in our opinion.

More details on the quality and contiguity of the assemblies should be provided, at least the N50 or the NG50 statistics, the number of scaffolds, and some QV statistics, like those produced by Merqury (Rhie et al. 2020)¹.

The title also claims that the genomes are complete, but the paper does not provide any metrics about it. Usually, short Illumina reads can not resolve the repetitive regions of the genome. We understand that the authors probably could not reach the chromosome-level due to technical limitations (e.g. Hi-C data to join the scaffolds seem not available), still, we suggest providing some measure of the completeness of their assemblies both at structural (k-mer completeness form Merqury) and functional (from Busco analysis (Manni et al. 2021)²) level. For similar reasons, we think that the title should be changed by replacing the term “complete” with “scaffold-level” as the latter describes the quality of the described genomes more accurately.

We also suggest adding more information about how samples were acquired (permissions and ethic statements). I am also concerned by the fact that the parrots can hybridize in captivity, so detailed information about the (potential) hybrid status of each individual should be provided.

We hope our suggestions can help the authors to further improve their paper.

Is the rationale for creating the dataset(s) clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Partly
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Partly

References

1. Rhie A, Walenz B, Koren S, Phillippy A: Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology. 2020; 21 (1). Publisher Full Text
2. Manni M, Berkeley MR, Seppey M, Simão FA, et al.: BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.Mol Biol Evol. 2021; 38 (10): 4647-4654 PubMed Abstract | Publisher Full Text

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Bird ecology (RA) and genomics (SS).

We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.

CITE

Report a concern

Respond or Comment

Views

23

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

https://doi.org/10.5256/f1000research.28208.r82331

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

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, detailed below:

The biggest limitation is the inability to link the genomic information with certainty to a taxonomic name because of the lack of a voucher specimen and uncertainty about the possible hybrid status of pet parrots. The samples come from either pet birds or birds in captive breeding programs. While birds in captive breeding programs are more likely to be genetically pure, pet parrots could come from anywhere (even the illegal pet trade). Parrot species are known to hybridize in introduced habitats, in the wild, and in captivity—and can even produce viable offspring between genera (Hernandez-Brito et al. 2021 in Ibis¹). More details on provenance might alleviate some concerns, but it will be hard to get away from some uncertainty about whether these genomes are accurate representations of their taxonomic identifiers.
The genomes are not complete, since the assemblies come from Illumina short reads and likely do not cover certain, more difficult regions of the genome. Information on depth of sequencing and contiguity (e.g., N50) is available on NCBI, but should also appear in the table to allow readers to assess genome quality more directly.
The introduction would be enriched by a little more information on the rationale for the study. Specifically, what is currently missing from parrots studies that these genomes could provide? Describe existing genomic resources and then narrow to a knowledge gap that the authors hope to fill with these genomes. Was there a rationale for the specific species chosen?
Likewise, the Discussion would benefit from more elaboration on the broad utility of these datasets, e.g., mapping whole genome re-sequence data or reduced representation sequence data for population genetics studies, etc. Specifically, which uses might not be diminished by some uncertainty surrounding taxonomic assignment?

Is the rationale for creating the dataset(s) clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Partly
Are sufficient details of methods and materials provided to allow replication by others?

No
Are the datasets clearly presented in a useable and accessible format?

Yes

References

1. Hernández‐Brito D, Tella J, Carrete M, Blanco G: Successful hybridization between non‐congeneric parrots in a small introduced population. Ibis. 2021. Publisher Full Text

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Phylogenetics, genomics, birds

We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.

CITE

Report a concern

Respond or Comment

Views

29

Reviewer Report 19 Feb 2021

Paweł Mackiewicz, Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland

Approved with Reservations

https://doi.org/10.5256/f1000research.28208.r77387

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

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 the genomes are complete, whereas the obtained sequences are not assembled and are still organized in scaffolds. Therefore, the title should be changed and the authors should describe in more detail the data set including information about incompleteness and gaps in the sequences. The limitations of the datasets should necessary be presented.
The authors should state which type of analyses can be performed on such incomplete data set and which further steps should be performed to assembly the sequences.
Could you answer for the following questions:
Which problems prevented the obtaining the complete genomes? Are the authors going to assembly and study these genomes in the future?
Moreover, the authors should present in detail sources for each studied sample, e.g. zoo, natural environment with detailed localization, individual breeders, reservation etc. It is essential. Describe in detail the captive breeding programs in the context of the samples, which you mentioned. Ethics policies should be also included. Were the samples obtained and transferred according to the species protection law? It should be clearly stated.
Although my review may seem harsh, actually I think that the obtained
genomic sequences are valuable for various studies and the data set is interesting for scientific community. I am very willing to accept the manuscript after the inclusion of information and explanations that I mentioned in my review.

Is the rationale for creating the dataset(s) clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Partly
Are sufficient details of methods and materials provided to allow replication by others?

Partly
Are the datasets clearly presented in a useable and accessible format?

Partly

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: bioinformatics, genomics, phylogenetics, molecular evolution

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

CITE

Report a concern

Respond or Comment

Comments on this article Comments (0)

Version 1

VERSION 1 PUBLISHED 12 Nov 2020

Open Peer Review

Reviewer Status

Reviewer Reports

	Invited Reviewers
	1	2	3
Version 1 12 Nov 20	read	read	read

Paweł Mackiewicz, University of Wrocław, Wrocław, Poland
Devon DeRaad, Kansas University, Kansas, USA

John McCormack, Occidental College, Los Angeles, USA
Roberto Ambrosini, University of Milan, via Celoria 26, Italy

Simona Secomandi, University of Milan, via Celoria 26, Italy

Comments on this article

All Comments(0)

Add a comment

Sign up for content alerts

Browse by related subjects

Back to all reports

Reviewer Report

10 Views

26 Oct 2021 | for Version 1

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

10 Views Cite this report Responses(0)

Approved With Reservations

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 are a series of points that we think can be improved.

Despite this work being published as a data note and no detailed results are therefore expected, the data description is too brief, in our opinion.

More details on the quality and contiguity of the assemblies should be provided, at least the N50 or the NG50 statistics, the number of scaffolds, and some QV statistics, like those produced by Merqury (Rhie et al. 2020)¹.

The title also claims that the genomes are complete, but the paper does not provide any metrics about it. Usually, short Illumina reads can not resolve the repetitive regions of the genome. We understand that the authors probably could not reach the chromosome-level due to technical limitations (e.g. Hi-C data to join the scaffolds seem not available), still, we suggest providing some measure of the completeness of their assemblies both at structural (k-mer completeness form Merqury) and functional (from Busco analysis (Manni et al. 2021)²) level. For similar reasons, we think that the title should be changed by replacing the term “complete” with “scaffold-level” as the latter describes the quality of the described genomes more accurately.

We also suggest adding more information about how samples were acquired (permissions and ethic statements). I am also concerned by the fact that the parrots can hybridize in captivity, so detailed information about the (potential) hybrid status of each individual should be provided.

We hope our suggestions can help the authors to further improve their paper.

Is the rationale for creating the dataset(s) clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Partly
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Partly

References

1. Rhie A, Walenz B, Koren S, Phillippy A: Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology. 2020; 21 (1). Publisher Full Text
2. Manni M, Berkeley MR, Seppey M, Simão FA, et al.: BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.Mol Biol Evol. 2021; 38 (10): 4647-4654 PubMed Abstract | Publisher Full Text

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Bird ecology (RA) and genomics (SS).

We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.

Respond to this report

Responses (0)

Back to all reports

Reviewer Report

23 Views

08 Apr 2021 | for Version 1

Devon DeRaad, Department of Ecology & Evolutionary Biology, Kansas University, Kansas, USA

John McCormack, Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA

23 Views Cite this report Responses(0)

Approved With Reservations

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, detailed below:

The biggest limitation is the inability to link the genomic information with certainty to a taxonomic name because of the lack of a voucher specimen and uncertainty about the possible hybrid status of pet parrots. The samples come from either pet birds or birds in captive breeding programs. While birds in captive breeding programs are more likely to be genetically pure, pet parrots could come from anywhere (even the illegal pet trade). Parrot species are known to hybridize in introduced habitats, in the wild, and in captivity—and can even produce viable offspring between genera (Hernandez-Brito et al. 2021 in Ibis¹). More details on provenance might alleviate some concerns, but it will be hard to get away from some uncertainty about whether these genomes are accurate representations of their taxonomic identifiers.
The genomes are not complete, since the assemblies come from Illumina short reads and likely do not cover certain, more difficult regions of the genome. Information on depth of sequencing and contiguity (e.g., N50) is available on NCBI, but should also appear in the table to allow readers to assess genome quality more directly.
The introduction would be enriched by a little more information on the rationale for the study. Specifically, what is currently missing from parrots studies that these genomes could provide? Describe existing genomic resources and then narrow to a knowledge gap that the authors hope to fill with these genomes. Was there a rationale for the specific species chosen?
Likewise, the Discussion would benefit from more elaboration on the broad utility of these datasets, e.g., mapping whole genome re-sequence data or reduced representation sequence data for population genetics studies, etc. Specifically, which uses might not be diminished by some uncertainty surrounding taxonomic assignment?

Is the rationale for creating the dataset(s) clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Partly
Are sufficient details of methods and materials provided to allow replication by others?

No
Are the datasets clearly presented in a useable and accessible format?

Yes

References

1. Hernández‐Brito D, Tella J, Carrete M, Blanco G: Successful hybridization between non‐congeneric parrots in a small introduced population. Ibis. 2021. Publisher Full Text

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Phylogenetics, genomics, birds

We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.

Respond to this report

Responses (0)

Back to all reports

Reviewer Report

29 Views

19 Feb 2021 | for Version 1

Paweł Mackiewicz, Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland

29 Views Cite this report Responses(0)

Approved With Reservations

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 the genomes are complete, whereas the obtained sequences are not assembled and are still organized in scaffolds. Therefore, the title should be changed and the authors should describe in more detail the data set including information about incompleteness and gaps in the sequences. The limitations of the datasets should necessary be presented.
The authors should state which type of analyses can be performed on such incomplete data set and which further steps should be performed to assembly the sequences.
Could you answer for the following questions:
Which problems prevented the obtaining the complete genomes? Are the authors going to assembly and study these genomes in the future?
Moreover, the authors should present in detail sources for each studied sample, e.g. zoo, natural environment with detailed localization, individual breeders, reservation etc. It is essential. Describe in detail the captive breeding programs in the context of the samples, which you mentioned. Ethics policies should be also included. Were the samples obtained and transferred according to the species protection law? It should be clearly stated.
Although my review may seem harsh, actually I think that the obtained
genomic sequences are valuable for various studies and the data set is interesting for scientific community. I am very willing to accept the manuscript after the inclusion of information and explanations that I mentioned in my review.

Is the rationale for creating the dataset(s) clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Partly
Are sufficient details of methods and materials provided to allow replication by others?

Partly
Are the datasets clearly presented in a useable and accessible format?

Partly

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

bioinformatics, genomics, phylogenetics, molecular evolution

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Respond to this report

Responses (0)

[1] Alonge M: Ragtag: Reference-guided genome assembly correction and scaffolding. GitHub Archive. 2020. Publisher Full Text

[2] Bankevich A, Nurk S, Antipov D, et al.: SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012; 19(5): 455–477. PubMed Abstract | Publisher Full Text | Free Full Text

[3] Berg ML, Bennett ATD: The evolution of plumage colouration in parrots: a review. Emu - Austral Ornithology. 2010; 110(1): 10–20. Publisher Full Text

[4] Bolger AM, Lohse M, Usadel B: Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. 2014; 30(15): 2114–20. PubMed Abstract | Publisher Full Text | Free Full Text

[5] Botelho JF, Smith-Paredes D, Nuñez-Leon D, et al.: The developmental origin of zygodactyl feet and its possible loss in the evolution of Passeriformes. Proc Biol Sci. 2014; 281(1788): 20140765. PubMed Abstract | Publisher Full Text | Free Full Text

[6] Butchart SH, Stattersfield AJ, Bennun LA, et al.: Measuring global trends in the status of biodiversity: red list indices for birds. PLoS Biol. 2004; 2(12): e383. PubMed Abstract | Publisher Full Text | Free Full Text

[7] Clements JF, Schulenberg TS, Iliff MJ, et al.: The eBird/Clements Checklist of Birds of the World: v2019. 2019. Reference Source

[8] National Research Council: Guide for the Care and Use of Laboratory Animals. Eighth edition, 2011. Reference Source

[9] Pepperberg IM: "Birdbrains" should not be ignored in studying the evolution of g. Behav Brain Sci. 2017; 40: e216. PubMed Abstract | Publisher Full Text

[10] Yang F, Ding F, Chen H, et al.: DNA barcoding for the identification and authentication of animal species in traditional medicine. Evid Based Complement Alternat Med. 2018; 2018: 5160254. PubMed Abstract | Publisher Full Text | Free Full Text

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

Abstract

Keywords

Editorial note

Introduction

Methods

Table 1. Species sequenced for this study.

Results

Data availability

Underlying data

References

Comments on this article Comments (0)

Open Peer Review

Comments on this article Comments (0)

Open Peer Review

Reviewer Status

Reviewer Reports

Comments on this article

Browse by related subjects

Competing Interests Policy

Stay Updated