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

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.

SUBMITTER: Lee H

PROVIDER: S-EPMC6999708 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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

Lee HyeJin H Kim Jungeun J Weber Jessica A JA Chung Oksung O Cho Yun Sung YS Jho Sungwoong S Jun JeHoon J Kim Hak-Min HM Lim Jeongheui J Choi Jae-Pil JP Jeon Sungwon S Blazyte Asta A Edwards Jeremy S JS Paek Woon Kee WK Bhak Jong J

Molecules and cells 20200101 1

The red-crowned crane (<i>Grus japonensis</i>) 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 evolu ...[more]

PMID: 31940721

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Project description:IntroductionAnimal intestines are extremely rich in microbial ecosystems. Numerous studies in different fields, such as epidemiology and histology, have revealed that gut microorganisms considerably mediate the survival and reproduction of animals. However, gut microbiology studies of homogeneously distributed wild cranes are still rare. This study aimed to understand the structural composition of the gut microbial community of wild cranes and elucidate the potential roles of the microorganisms.MethodsWe used high-throughput sequencing to analyze the gut microbial community structure of wild cranes in the Zhalong Nature Reserve.ResultsA total of 1,965,683 valid tags and 5248 OTUs were obtained from 32 fecal samples. Twenty-six bacteria phyla and 523 genera were annotated from the intestinal tract of the red-crowned crane. Twenty-five bacteria phyla and 625 genera were annotated from the intestine of the white-naped crane. Firmicutes, Proteobacteria, and Bacteroidetes are the dominant bacterial phyla in the intestinal tract of red-crowned cranes, while Catellicoccus, Lactobacillus, Neisseria, and Streptococcus were the dominant genera. The dominant bacterial phyla in the intestinal tract of white-naped cranes were Firmicutes, Proteobacteria, Bacteroidetes, Epsilonbacteraeota, Actinobacteria, and Fusobacteria. However, the dominant genera were Catellicoccus, Lactobacillus, Neisseria, Campylobacter, Streptococcus, Anaerobiospirillum, Romboutsia, Turicibacter, Haemophilus, and Lautropia. Firmicutes had significantly higher relative abundance in the intestine of the red-crowned than white-naped cranes (P < 0.05). However, the relative abundance of Actinobacteria and Bacteroidetes was significantly higher (P < 0.05) in the intestines of white-naped than red-crowned cranes. The diversity of the intestinal flora between the two crane species was significantly different (P < 0.05). Besides, the alpha diversity of the intestinal flora was higher for white-naped than red-crowned cranes. Eight of the 41 functional pathways differed in the gut of both crane species (P < 0.05).DiscussionBoth species live in the same area and have similar feeding and behavioral characteristics. Therefore, host differences are possibly the main factors influencing the structural and functional differences in the composition of the gut microbial community. This study provides important reference data for constructing a crane gut microbial assessment system. The findings have implications for studying deeper relationships between crane gut microbes and genetics, nutrition, immunity, and disease.

Dataset Information

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

Publications

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

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