A chromosome‐level genome of <i>Antechinus flavipes</i> provides a reference for an Australian marsupial genus with male death after mating

Tian, Ran; Han, Kai; Geng, Yuepan; Yang, Chen; Shi, Chengcheng; Thomas, Patrick B.; Pearce, Coral; Moffatt, Kate; Ma, Siming; Xu, Shixia; Zhou, Xuming; Gladyshev, Vadim N.; Liu, Xin; Fisher, Diana O.; Chopin, Lisa K.; Leiner, Natália Oliveira; Baker, Andrew; Fan, Guangyi; Seim, Inge

doi:10.1111/1755-0998.13501

Cited by 14 publications

(20 citation statements)

References 133 publications

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“…Interspersed repeats constituted ~56% of the assembly (Supplementary Table 5). Consistent with the highly conserved genome organization of dasyuromorphs, the thylacine had similar overall repeat composition to its living relatives (Tian, et al 2022). The dominant repeat class was LINE elements (~36.5%), occurring at a frequency comparable to that of the Tasmanian devil (~39%), though somewhat lower than that of the brown antechinus (~45%) (Tian, et al 2022).…”

Section: Resultssupporting

confidence: 64%

“…Consistent with the highly conserved genome organization of dasyuromorphs, the thylacine had similar overall repeat composition to its living relatives (Tian, et al 2022). The dominant repeat class was LINE elements (~36.5%), occurring at a frequency comparable to that of the Tasmanian devil (~39%), though somewhat lower than that of the brown antechinus (~45%) (Tian, et al 2022). Interestingly, we observed that LTRs were sparse in the thylacine genome (~1.51%) compared to previously studied marsupial species (which ranged from 6.53%-18.89%; Supplementary Table 5) (Tian, et al 2022).…”

Section: Repeat Classification and Genome Annotationsupporting

confidence: 60%

“…The copyright holder for this preprint this version posted March 3, 2022. ; https://doi.org/10.1101/2022.03.02.482690 doi: bioRxiv preprint though somewhat lower than that of the brown antechinus (~45%) (Tian, et al 2022).…”

Section: Repeat Classification and Genome Annotationmentioning

confidence: 92%

“…These results were compared with several recent de novo marsupial genome assemblies (Fig. 1e, Supplementary Tables 3 and 4) (Brandies, et al 2020; Dudchenko, et al 2017; Johnson, et al 2018; Peel, et al 2022; Seppey, et al 2019; Tian, et al 2022). Comparison genomes were chosen to represent a variety of marsupial lineages and assembly approaches released within the past 4 years.…”

Section: Methodsmentioning

confidence: 99%

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A chromosome-scale hybrid genome assembly of the extinct Tasmanian tiger (Thylacinus cynocephalus)

Feigin

Frankenberg

Pask

2022

Preprint

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The extinct Tasmanian tiger or thylacine (Thylacinus cynocephalus) was a large marsupial carnivore native to Australia. Once ranging across parts of the mainland, the species remained only on the island of Tasmania by the time of European colonization. It was driven to extinction in the early 20th century and is an emblem of native species loss in Australia. The thylacine was a striking example of convergent evolution with placental canids, with which it shared a similar skull morphology. Consequently, it has been the subject of extensive study. While the original thylacine assemblies published in 2018 enabled the first exploration of the species’ genome biology, further progress is hindered by the lack of high-quality genomic resources. Here, we present a new chromosome-scale hybrid genome assembly for the thylacine, which compares favorably with many recent de novo marsupial genomes. Additionally, we provide homology-based gene annotations, characterize the repeat content of the thylacine genome and show that, consistent with demographic decline, the species possessed a low rate of heterozygosity even compared to extant, threatened marsupials.SignificanceThe lack of high-quality genomes for extinct species inhibits research into their biology. Moreover, marsupials are underrepresented among sequenced genomes. Here, we present a new, chromosome-scale thylacine genome. This high-quality assembly is a valuable new resource for studies on marsupial carnivores.

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Section: Resultssupporting

confidence: 64%

Section: Repeat Classification and Genome Annotationsupporting

confidence: 60%

Section: Repeat Classification and Genome Annotationmentioning

confidence: 92%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

A chromosome-scale hybrid genome assembly of the extinct Tasmanian tiger (Thylacinus cynocephalus)

Feigin

Frankenberg

Pask

2022

Preprint

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“…Similar phenomenon has been observed in mammals. Male pouched mice ( Antechinus ) experience severe hormonal disbalance during the mating period that results in their death at the end of mating period [ 73 ].…”

Section: Altruismmentioning

confidence: 99%

Altruism and Phenoptosis as Programs Supported by Evolution

Shilovsky

Putyatina

Марков

2021

Biochemistry Moscow

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Phenoptosis is a programmed death that has emerged in the process of evolution, sometimes taking the form of an altruistic program. In particular, it is believed to be a weapon against the spread of pandemics in the past and an obstacle in fighting pandemics in the present (COVID). However, on the evolutionary scale, deterministic death is not associated with random relationships (for example, bacteria with a particular mutation), but is a product of higher nervous activity or a consequence of established hierarchy that reaches its maximal expression in eusocial communities of Hymenoptera and highly social communities of mammals. Unlike a simple association of individuals, eusociality is characterized by the appearance of non-reproductive individuals as the highest form of altruism. In contrast to primitive programs for unicellular organisms, higher multicellular organisms are characterized by the development of behavior-based phenoptotic programs, especially in the case of reproduction-associated limitation of lifespan. Therefore, we can say that the development of altruism in the course of evolution of sociality leads in its extreme manifestation to phenoptosis. Development of mathematical models for the emergence of altruism and programmed death contributes to our understanding of mechanisms underlying these paradoxical counterproductive (harmful) programs. In theory, this model can be applied not only to insects, but also to other social animals and even to the human society. Adaptive death is an extreme form of altruism. We consider altruism and programmed death as programmed processes in the mechanistic and adaptive sense, respectively. Mechanistically, this is a program existing as a predetermined chain of certain responses, regardless of its adaptive value. As to its adaptive value (regardless of the degree of “phenoptoticity”), this is a characteristic of organisms that demonstrate high levels of kinship, social organization, and physical association typical for higher-order individuals, e.g., unicellular organisms forming colonies with some characteristics of multicellular animals or colonies of multicellular animals displaying features of supraorganisms.

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Modalities of aging in organisms with different strategies of resource allocation

Suvorov

2022

Ageing Research Reviews

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A chromosome‐level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution-NonCo mmercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 14 publications

References 133 publications

A chromosome-scale hybrid genome assembly of the extinct Tasmanian tiger (Thylacinus cynocephalus)

A chromosome-scale hybrid genome assembly of the extinct Tasmanian tiger (Thylacinus cynocephalus)

Altruism and Phenoptosis as Programs Supported by Evolution

Modalities of aging in organisms with different strategies of resource allocation

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