TY - JOUR

T1 - Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation

AU - Kolchanova, Sofiia

AU - Kliver, Sergei

AU - Кливер, Сергей

AU - Komissarov, Aleksei

AU - Dobrinin, Pavel

AU - Tamazian, Gaik

AU - Grigorev, Kirill

AU - Wolfsberger, Walter W.

AU - Majeske, Audrey J.

AU - Velez-Valentin, Jafet

AU - de la Rosa, Valentin

AU - Paul-Murphy, Joanne R.

AU - Guzman, David S.-M.

AU - Court, Michael H.

AU - Rodriguez-Flores, Juan L.

AU - Martinez-Cruzado, Juan C.

AU - Oleksyk, Taras K.

N1 - Kolchanova, S.; Kliver, S.; Komissarov, A.; Dobrinin, P.; Tamazian, G.; Grigorev, K.; Wolfsberger, W.W.; Majeske, A.J.; Velez-Valentin, J.; Valentin de la Rosa, R.; Paul-Murphy, J.R.; Guzman, D.S.-M.; Court, M.H.; Rodriguez-Flores, J.L.; Martínez-Cruzado, J.C.; Oleksyk, T.K. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. Genes 2019, 10, 54.

PY - 2019/1/16

Y1 - 2019/1/16

N2 - 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.

AB - 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.

KW - Birds

KW - Conservation

KW - Cuba

KW - Demography

KW - Genomics

KW - Heterozygosity

KW - Hispaniola

KW - Parrots

KW - Puerto Rican parrot

UR - http://www.scopus.com/inward/record.url?scp=85060697342&partnerID=8YFLogxK

UR - https://www.mdpi.com/2073-4425/10/1/54

UR - https://elibrary.ru/item.asp?id=38656980

U2 - doi: 10.3390/genes10010054.

DO - doi: 10.3390/genes10010054.

M3 - Article

VL - 10

JO - Genes

JF - Genes

SN - 2073-4425

IS - 1

M1 - 54

ER -