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Genes 2018, 9(8), 393; https://doi.org/10.3390/genes9080393

A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaiiʻs Last Remaining Crow Species

1
Department of Biology, University of Hawaii at Hilo, Hilo, HI 96720, USA
2
Institute for Conservation Research, San Diego Zoo, Escondido, CA 92027, USA
3
Pacific Biosciences, Menlo Park, CA 94025, USA
4
Institute for Conservation Research, San Diego Zoo Global, Volcano, HI 96785, USA
*
Author to whom correspondence should be addressed.
Received: 6 June 2018 / Revised: 23 July 2018 / Accepted: 27 July 2018 / Published: 1 August 2018
(This article belongs to the Special Issue Conservation Genetics and Genomics)
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Abstract

Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the ʻAlalā (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawaiʻi, the ʻAlalā survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the ʻAlalā genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications. View Full-Text
Keywords: runs of homozygosity (ROH); inbreeding depression; major histocompatibility complex; toll-like receptors; behavior; SMRT sequencing runs of homozygosity (ROH); inbreeding depression; major histocompatibility complex; toll-like receptors; behavior; SMRT sequencing
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Sutton, J.T.; Helmkampf, M.; Steiner, C.C.; Bellinger, M.R.; Korlach, J.; Hall, R.; Baybayan, P.; Muehling, J.; Gu, J.; Kingan, S.; Masuda, B.M.; Ryder, O.A. A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaiiʻs Last Remaining Crow Species. Genes 2018, 9, 393.

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