Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises

Çilingir, F. Gözde; Hansen, Dennis M.; Bunbury, Nancy; Postma, Erik; Baxter, Richard H. G.; Turnbull, Lindsay A.; Özgül, Arpat; Grossen, Christine

doi:10.1101/2021.11.08.467072

Cited by 2 publications

(1 citation statement)

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“…We used ANGSD v0.93 (ANGSD, RRID:SCR_021865) [110,111] to produce genotype likelihoods appropriate for the low coverage of individual samples. GATK was used (GATK, RRID:SCR_001876) [109] to infer major and minor alleles from the likelihoods (doMajorMinor 1, doMaf 1).…”

Section: Data Filtering Alignment and Genotype Likelihood Estimationmentioning

confidence: 99%

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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Section: Data Filtering Alignment and Genotype Likelihood Estimationmentioning

confidence: 99%

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

Self Cite

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Еconomic development of the United Republic of Tanzania

Ignatiev,

Zaporizka

2023

Journal of Economics and International Relations

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Achieving balanced economic growth is one of the priorities of governments in developing countries. This is especially relevant for certain African countries that have such characteristics as a favorable geographical location and considerable demographic resource. The policy of the United Republic of Tanzania is an example of successful strategy, since the country not only demonstrates a dynamic growth of GDP, but also competes for regional leadership with neighboring Kenya. The object is the economic policy of Tanzania, while the subject is represented by national interests, resources, and the tools of management of processes of national economic growth. Because of this the article aims at establishing comparative advantages of Tanzania and the peculiarities of its economic advancement. The system approach is used in the article, since it analyzes the economic policy as the set of elements that interact with each other. It was found that Tanzania is a strategic player in East Africa in terms of logistics that at the same time enjoys an appropriate tourism potential, represented by Mount Kilimanjaro, the national parks of international importance, and the popular islands in the Indian Ocean. The basis of the national economic strategy is the focus on transport and tourist services, which can be considered rather unusual for the African continent. At the same time, Tanzania is trying to effectively use its opportunities in the fields of agriculture and mining industry and is also actively developing transport infrastructure in order to become a logistics hub in the region. Moreover, the country is taking steps to exploit the commercial reserves of oil and natural gas. Tanzania’s foreign economic ties play an important role. This state actor has Chinese orientation since Beijing is its main trading partner and a major investor in infrastructure projects. Tanzanian political elite is also actively diversifying its contacts by deepening the cooperation with Türkiye. The complex of these factors helps to ensure balanced economic development, as well as to gain certain advantages in the competition with Kenya for the leadership in the East African region.

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Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises

Cited by 2 publications

References 76 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

Еconomic development of the United Republic of Tanzania

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