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, 43 (1), 86-95

Whole Genome Analysis of the Red-Crowned Crane Provides Insight Into Avian Longevity

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Whole Genome Analysis of the Red-Crowned Crane Provides Insight Into Avian Longevity

HyeJin Lee et al. Mol Cells.

Abstract

The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane's long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified redcrowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH , RPA1, PHAX, HNMT , HS2ST1 , PPCDC , PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species.

Keywords: genome; longevity; red-crowned crane.

Conflict of interest statement

Disclosure

O.C., Y.S.C., and J.J. are employees and J.B. is one of the founders of Clinomics Ltd. All other authors have no potential conflicts of interest to disclose.

Figures

Fig. 1
Fig. 1. Orthologous gene clusters of the red-crowned crane compared to the other avian species
(A) The Venn diagram shows the number of unique (number in the ovals) and shared (the number in the center black circle) gene families analyzed by OrthoMCL (Li et al., 2003). It was drawn manually using the online photo editor (https://pixlr.com/editor/). (B) Divergence time of the red-crowned-crane and grey-crowned crane (Hedges et al., 2015).
Fig. 2
Fig. 2. Functional analysis of the red-crowned crane PSGs
(A) Red-crowned crane PSGs enriched in GO categories. The values to the right of the bar represent the p-values from the enrichment test analyzed on the DAVID website (Huang et al., 2008). (B) Network diagram of the red-crowned crane PSGs associated with KEGG pathways. The blue rectangles represent pathway IDs from the KEGG database and the green circles represent the red-crowned crane PSGs. Each edge represents the association between the pathways and the genes.
Fig. 3
Fig. 3. Demographic history of the red-crowned crane and grey-crowned crane
PSMC demographic modeling of the red-crowned crane, using a generation time (g = 12.3 years) and mutation rate per generation time (μ = 9.66 × 10−9), and the grey-crowned crane, with a generation time (g = 15.1) and mutation rate (μ = 1.18 × 10−8). Tsuf, atmospheric surface air temperature; RSL, relative sea level; 10 m.s.l.e., 10 m sea level equivalent.

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