Genomes of three closely related caribbean amazons provide insight for species history and conservation

Sofiia Kolchanova, Sergei Kliver, Aleksei Komissarov, Pavel Dobrinin, Gaik Tamazian, Kirill Grigorev, Walter W. Wolfsberger, Audrey J. Majeske, Jafet Velez-Valentin, Ricardo Valentin de la Rosa, Joanne R Paul-Murphy, David Guzman, Michael H. Court, Juan L. Rodriguez-Flores, Juan Carlos Martínez-Cruzado, Taras K. Oleksyk

Research output: Contribution to journalArticle

Abstract

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.

Original languageEnglish (US)
Article number54
JournalGenes
Volume10
Issue number1
DOIs
StatePublished - Jan 1 2019

Fingerprint

Amazona
Parrots
History
Genome
Islands
Finches
Genome Size
Transcriptome
Human Activities
Birds
Demography
Genes

Keywords

  • Birds
  • Conservation
  • Cuba
  • Demography
  • Genomics
  • Heterozygosity
  • Hispaniola
  • Parrots
  • Puerto Rican parrot

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Kolchanova, S., Kliver, S., Komissarov, A., Dobrinin, P., Tamazian, G., Grigorev, K., ... Oleksyk, T. K. (2019). Genomes of three closely related caribbean amazons provide insight for species history and conservation. Genes, 10(1), [54]. https://doi.org/10.3390/genes10010054

Genomes of three closely related caribbean amazons provide insight for species history and conservation. / Kolchanova, Sofiia; Kliver, Sergei; Komissarov, Aleksei; Dobrinin, Pavel; Tamazian, Gaik; Grigorev, Kirill; Wolfsberger, Walter W.; Majeske, Audrey J.; Velez-Valentin, Jafet; de la Rosa, Ricardo Valentin; Paul-Murphy, Joanne R; Guzman, David; Court, Michael H.; Rodriguez-Flores, Juan L.; Martínez-Cruzado, Juan Carlos; Oleksyk, Taras K.

In: Genes, Vol. 10, No. 1, 54, 01.01.2019.

Research output: Contribution to journalArticle

Kolchanova, S, Kliver, S, Komissarov, A, Dobrinin, P, Tamazian, G, Grigorev, K, Wolfsberger, WW, Majeske, AJ, Velez-Valentin, J, de la Rosa, RV, Paul-Murphy, JR, Guzman, D, Court, MH, Rodriguez-Flores, JL, Martínez-Cruzado, JC & Oleksyk, TK 2019, 'Genomes of three closely related caribbean amazons provide insight for species history and conservation', Genes, vol. 10, no. 1, 54. https://doi.org/10.3390/genes10010054
Kolchanova S, Kliver S, Komissarov A, Dobrinin P, Tamazian G, Grigorev K et al. Genomes of three closely related caribbean amazons provide insight for species history and conservation. Genes. 2019 Jan 1;10(1). 54. https://doi.org/10.3390/genes10010054
Kolchanova, Sofiia ; Kliver, Sergei ; Komissarov, Aleksei ; Dobrinin, Pavel ; Tamazian, Gaik ; Grigorev, Kirill ; Wolfsberger, Walter W. ; Majeske, Audrey J. ; Velez-Valentin, Jafet ; de la Rosa, Ricardo Valentin ; Paul-Murphy, Joanne R ; Guzman, David ; Court, Michael H. ; Rodriguez-Flores, Juan L. ; Martínez-Cruzado, Juan Carlos ; Oleksyk, Taras K. / Genomes of three closely related caribbean amazons provide insight for species history and conservation. In: Genes. 2019 ; Vol. 10, No. 1.
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