The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758

Chang, Glenn; Jones, Samantha; Leelakumari, Sreeja; Ashkani, Jahanshah; Culibrk, Luka; O’Neill, Kieran; Tse, Kane; Cheng, Dean; Chuah, Eric; McDonald, Helen; Kirk, Heather; Pandoh, Pawan; Pari, Sauro; Angelini, Valeria; Kyle, Christopher J.; Bertorelle, Giorgio; Zhao, Yongjun; Mungall, Andrew J.; Moore, Richard A.; Vilaça, Sibelle Torres; Jones, Steven J.M.

doi:10.12688/f1000research.131283.2

Cited by 4 publications

(3 citation statements)

References 28 publications

(38 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The BUSCO scores based on the sauropsida _odb10 (95.5%) and vertebrata_odb10 (98.3%) lineage databases were also all above 95%. We compared the genome completeness by Busco score and contig N50 length with 13 published turtle genomes, Including Pelodiscus sinensis (GCF_000230535) 19 , Chelonia mydas (GCF_015237465) 19 , Rafetus swinhoei (GCA_019425775.1) 20 , Caretta caretta (GCF_023653815) 21 , Pelochelys cantorii (GCA_032595735.1) 22 , Dermochelys coriacea (GCF_009764565.3) 23 , Chelydra serpentina (GCA_018859375.1) 24 , Dermatemys mawii (GCA_007922305.1), Gopherus flavomarginatus (GCF_025201925.1), Mauremys mutica (GCF_020497125) 25 , Platysternon megacephalum (GCA_003942145.1) 26 , Trachemys scripta elegans (GCF_013100865.1) 27 and Podocnemis expansa (GCA_007922195.1) 28 from NCBI. Our assembly is comparable to the achievements observed in other genomes (Fig.…”

Section: Methodsmentioning

confidence: 99%

A chromosome-level genome assembly of the pig-nosed turtle (Carettochelys insculpta)

Li,

Liu,

Zheng

et al. 2024

Sci Data

View full text Add to dashboard Cite

The pig-nosed turtle (Carettochelys insculpta) represents the only extant species within the Carettochelyidae family, is a unique Trionychia member fully adapted to aquatic life and currently facing endangerment. To enhance our understanding of this species and contribute to its conservation efforts, we employed high-fidelity (HiFi) and Hi-C sequencing technology to generate its genome assembly at the chromosome level. The assembly result spans 2.18 Gb, with a contig N50 of 126 Mb, encompassing 34 chromosomes that account for 99.6% of the genome. The assembly has a BUSCO score above 95% with different databases and strong collinearity with Yangtze giant softshell turtles (Rafetus swinhoei), indicating its completeness and continuity. A total of 19,175 genes and 46.86% repetitive sequences were annotated. The availability of this chromosome-scale genome represents a valuable resource for the pig-nosed turtle, providing insights into its aquatic adaptation and serving as a foundation for future turtle research.

show abstract

Section: Methodsmentioning

confidence: 99%

A chromosome-level genome assembly of the pig-nosed turtle (Carettochelys insculpta)

Li,

Liu,

Zheng

et al. 2024

Sci Data

View full text Add to dashboard Cite

show abstract

“…We processed the 2bRAD sequences using customized scripts 39 , trimming the raw sequences to remove ligation adaptors and cutting all the fragments to the same length (34 bp). We mapped the trimmed sequences to the published reference genome of the loggerhead turtle (GenBank accession GCA_023653815.1) 85 using Hisat2-2.2.1 86 , to identify polymorphic nucleotides (SNPs) with BCFtools 87 . Individual genotypes were outputted as SNPs in a VCF file.…”

Section: Methodsmentioning

confidence: 99%

New colonisers drive the increase of the emerging loggerhead turtle nesting in Western Mediterranean

Luna-Ortiz,

Marín-Capuz,

Abella

et al. 2024

Sci Rep

View full text Add to dashboard Cite

The loggerhead sea turtle (Caretta caretta) is sensitive to climate change and is responding by colonising the Western Mediterranean. To understand the rapid nesting increase in recent years in Spain, we sampled 45 hatchlings from 8 nests between 2016 and 2019. We sequenced a mtDNA D‐loop region, genotyped 2291 SNPs using 2bRAD and collected data on clutch size, hatching success, and incubation duration. We confirmed that the colonisation has a Mediterranean and Atlantic mixed origin and we detected that these nests were laid by different females, except for two nests within the same season. Our results suggest that the recent increase in nesting is due to an increase in the number of colonising individuals rather than females born in the same area returning to breed. We hypothesize that this increase in the number of colonisers results from successful conservation efforts, feminisation of the populations of origin and earlier sexual maturation. However, the percentage of offspring females produced in Spain suggests that future returning individuals will aid to the settlement of the new population. These results allow defining the current status of this colonisation although future efforts are needed to detect remigrants to confirm the establishment of a resident population.

show abstract

“…We envisaged a 1 × target nuclear genome coverage for all samples in order to obtain a high depth coverage (> 200 ×) for the mitochondrial DNA, which is represented by a much higher number of copies per cell than nuclear DNA (Michaels et al 1982;Robin and Wong 1988;Wiesner et al 1992). Considering a nuclear DNA genome size of 2.13 Gb (Chang et al 2023) and a mtDNA genome size of 16,737 bp for C. caretta (Drosopoulou et al 2012), we sequenced the libraries paired-end on an Illumina NovaSeq 6000 System using a 300-cycle NovaSeq 6000 SP Reagent Kit v 1.5 for an expected yield of approximately 250 Gb.…”

Section: Sampling Dna Isolation and Sequencing By Synthesismentioning

confidence: 99%

Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Tolve,

Iannucci,

Garofalo

et al. 2023

Mar Biol

View full text Add to dashboard Cite

Population structure and phylogeography of the loggerhead sea turtle (Caretta caretta) have so far been assessed mainly by mitochondrial DNA (mtDNA) single-gene sequencing studies. However, phylogenetic relationships amongst matrilines, genetic characterisation of rookeries and mixed-stock analyses have suffered from the limited resolution obtained by comparison of relatively short sequences such as from the mtDNA control region. Whole mitogenome sequencing can significantly improve population genetics, particularly in marine organisms showing female natal philopatry. Despite mitogenomics becoming increasingly common in biodiversity monitoring and conservation, only a few complete mitogenomes are available for C. caretta. In this study, we sequenced the complete mtDNA of 61 loggerhead turtles sampled between 2008 and 2021 along the Italian coastline and central Mediterranean Sea. We assigned complete mtDNA haplotypes to dead embryos and bycatch samples, and introduced a first nomenclature for loggerhead mitogenomes. Analysis of mtDNA diversity, Maximum Parsimony and Bayesian phylogenetic reconstruction allowed improved resolution of lineages with respect to studies reporting on partial mtDNA control region sequence comparisons, and we were able to further inform previous analyses on loggerhead ancestry based on control region haplogroups. Overall, whole mitogenome analysis has potential for considerable improvement of evolutionary history and phylogeographic investigations as well as mixed-stock surveys of loggerhead turtles.

show abstract

The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758

Cited by 4 publications

References 28 publications

A chromosome-level genome assembly of the pig-nosed turtle (Carettochelys insculpta)

A chromosome-level genome assembly of the pig-nosed turtle (Carettochelys insculpta)

New colonisers drive the increase of the emerging loggerhead turtle nesting in Western Mediterranean

Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Contact Info

Product

Resources

About