Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian

Abstract

Simple Summary The southern giant petrel Macronectes giganteus is one of key species on the Antarctic and sub-Antarctic regions. We reported the whole genome of M. giganteus for understanding the evolutionary mechanisms on Antarctic environments and for studying a more effective genetic monitoring of threatened species. The M. giganteus genome was 1.248 Gb in size with a scaffold N50 length of 27.4 Mb and a longest scaffold length of 120.4 Mb, and its genome contains 14,993 predicted protein-coding genes. The estimated historical effective population size of southern giant petrel underwent a severe reduction during a period coinciding with the early Pleistocene. The M. giganteus showed genomic expansion related to maintenance of energy homeostasis, being essential for survival and effective functioning in cold environments. Moreover, we employed a classification of microsatellite markers for studying the genetic diversity within and among populations. Genomic research of this first Antarctic bird helps to address the environmental adaptation and evolution of avian species. The southern giant petrel Macronectes giganteus, a large seabird of the southern oceans, is one of only two members of the genus Macronectes and is the largest species in the order Procellariiformes. Although these two families account for the vast majority of the avian fauna inhabiting the Antarctic and sub-Antarctic regions, studies on the status of some populations and the associated genetic data are currently extremely limited. In this study, we assembled the genome of M. giganteus by integrating Pacific Biosciences single-molecule real-time sequencing and the Chromium system developed by 10x Genomics. The final M. giganteus genome assembly was 1.248 Gb in size with a scaffold N50 length of 27.4 Mb and a longest scaffold length of 120.4 Mb. The M. giganteus genome contains 14,993 predicted protein-coding genes and has 11.06% repeat sequences. Estimated historical effective population size analysis indicated that the southern giant petrel underwent a severe reduction in effective population size during a period coinciding with the early Pleistocene. The availability of this newly sequenced genome will facilitate more effective genetic monitoring of threatened species. Furthermore, the genome will provide a valuable resource for gene functional studies and further comparative genomic studies on the life history and ecological traits of specific avian species.