Genomic insights into the evolution of the critically endangered soft‐shelled turtle <i>Rafetus swinhoei</i>

Ren, Yandong; Zhang, Qiang; Yan, Xiahui; Hou, Dongmin; Huang, He; Li, Chunhui; Rao, Dingqi; Li, Yongxin

doi:10.1111/1755-0998.13596

Cited by 10 publications

(14 citation statements)

References 91 publications

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“…The high ratio of syntenic regions that we found is between chelonian taxa that diverged around 50 to 70 million years ago (mya) [ 104 ] (Fig. 2 ) and is in agreement with previous studies, where the base substitution rate (evolutionary rate) of chelonians was found to be relatively low ([ 105 , 106 ]; see [ 107 ]).…”

Section: Data Descriptionsupporting

confidence: 92%

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Çilingir

A'Bear²,

Hansen

et al. 2022

GigaScience

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Background The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is listed as Vulnerable on the International Union for Conservation of Nature Red List (v2.3) due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts for both wild and ex situpopulations. A high-quality genome would also open avenues to investigate the genetic basis of the species’ exceptionally long life span. Findings We produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture. We produced a 2.37-Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNA sequencing–assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. To assess the utility of the high-quality assembly for species conservation, we performed a low-coverage resequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. We further identified putatively deleterious mutations to be monitored. Conclusions We establish a high-quality chromosome-level reference genome for A. gigantea and one of the most complete turtle genomes available. We show that low-coverage whole-genome resequencing, for which alignment to the reference genome is a necessity, is a powerful tool to assess the population structure of the wild population and reveal the geographic origins of ex situ individuals relevant for genetic diversity management and rewilding efforts.

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Section: Data Descriptionsupporting

confidence: 92%

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Çilingir

A'Bear²,

Hansen

et al. 2022

GigaScience

View full text Add to dashboard Cite

show abstract

“…The high ratio of syntenic regions that we found are between chelonian taxa that diverged around 50-70 mya [93] (Fig. 2) and is in agreement with previous studies, where the base substitution rate (evolutionary rate) of chelonians was found to be relatively low (see [94]).…”

Section: Synteny Analysissupporting

confidence: 93%

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Çilingir

A'Bear²,

Hansen

et al. 2022

Preprint

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The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is considered vulnerable due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts focused on both wild and ex-situ populations. A high-quality genome would also open avenues to investigate the genetic basis of the exceptionally long lifespan. Here, we produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture (Hi-C). We produced a 2.37 Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNAseq-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. We also performed a low-coverage re-sequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. The high-quality chromosome-level reference genome for A. gigantea is one of the most complete turtle genomes available. It is a powerful tool to assess the population structure in the wild population and reveal the geographic origins of ex-situ individuals relevant for genetic diversity management and rewilding efforts.

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“…Artificial breeding plays an important and positive role in the conservation of endangered turtle populations. Aside from the failure of artificial assisted breeding with 2 R. swinhoei (one female and one male; the female turtle died during artificial induction in 2019) [ 8 ], other turtle species have been successfully artificially bred. More successful species, such as Platuysternon megacephalum [ 9 ] and Mauremys mutica [ 10 ], have played an important role in the growth of turtle populations.…”

Section: Discussionmentioning

confidence: 99%

Status and Analysis of Artificial Breeding and Management of Aquatic Turtles in China

Hong

Zhang²,

Liu

et al. 2022

Biology

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China is a major country in turtle cultivation and has a long history of artificial breeding of turtles. In this study, a census and statistical analysis of artificially domesticated aquatic turtles in 15 provinces of China were conducted. The results showed that 29 species were aquatic turtles native to China, accounting for approximately 9% of the world’s total, and a large number of exotic aquatic turtles are also domesticated in China. The present situation of artificial breeding and protection of aquatic turtles in major provinces of China is shown, and existing problems are also put forward, with suggestions for the protection and management of aquatic turtles.

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Genomic insights into the evolution of the critically endangered soft‐shelled turtle Rafetus swinhoei

Cited by 10 publications

References 91 publications

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Status and Analysis of Artificial Breeding and Management of Aquatic Turtles in China

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