The first<i>Antechinus</i>reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies

Brandies, Parice A.; Tang, Simon; Johnson, Robert; Hogg, Carolyn J.; Belov, Katherine

doi:10.1101/2020.09.21.305722

Cited by 8 publications

(19 citation statements)

References 92 publications

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“…We annotated 24,708 A. flavipes protein-coding genes (82.2% supported by transcriptome data from 13 tissues). The A. flavipes reference assembly obtained a BUSCO (Benchmarking Universal Single-Copy Orthologs) (Seppey et al, 2019) genome completeness score of 92.4%) -comparable to A. stuartii (92.2% and 92.3% for a female and male assembly, respectively) (Brandies et al, 2020a), the koala (Phascolarctos cinereus ; 93.9%) (Johnson et al, 2018), and the S . harrisii (91.6%; 2019 assembly mSarHar1.1) (Table S7 ).…”

Section: Genome Assembly and Annotationmentioning

confidence: 92%

“…Genome sequences of other marsupials were also interrogated using the repeat element annotation pipeline. The following were downloaded from DNA Zoo [Virginia opossum (Didelphis virginiana ;dv-2k (Olga Dudchenko et al, 2018))], the NCBI Reference Sequence Database (Release 86) (Pruitt, Tatusova, & Maglott, 2007) [gray short-tail opossum (Monodelphis domestica ; MonDom5; GCF 000002295.2), koala (Phascolarctos cinereus ; phaCinunsw v4.1; GCA 002099425.1), Tasmanian devil (Sarcophilus harrisii; Devil ref v7.0, also known as sarHar1; GCA 000189315.1), Tammar wallaby (Notamacropus eugenii ; Meug 1.1; GCA 000004035.1), and common wombat (Vombatus ursinus ; GCF 900497805.2)], and the GigaScience Database [brown antechinus (Antechinus stuartii ; (Brandies et al, 2020a;Brandies, Tang, Johnson, Hogg, & Belov, 2020b)].…”

Section: Repeat Element Annotationmentioning

confidence: 99%

“…To investigate the phylogeny, demographic history, and genomic diversity of A. flavipes and to pave the way to understanding the evolution of semelparity, high-quality genomic data is required. A genome assembly of the brown antechinus (A. stuartii ) was recently reported (Brandies, Tang, Johnson, Hogg, & Belov, 2020a). However, a chromosome-level genome is not yet available.…”

Section: Introductionmentioning

confidence: 99%

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A chromosome-level genome of Antechinus flavipes provides a reference for an Australasian marsupial genus with suicidal reproduction

Tian¹,

Han²,

Geng³

et al. 2021

Preprint

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The 15 species of small carnivorous marsupials that comprise the genus Antechinus exhibit semelparity, a rare life-history strategy where death occurs after one breeding season. Antechinus males, but not females, age rapidly (demonstrate organismal senescence) during the breeding season and show promise as new animal models of ageing. Some antechinus species are also threatened or endangered. Here, we report chromosome-level genomes of the yellow-footed antechinus Antechinus flavipes. The genome assembly has a total length of 3.2 Gb with a contig N50 of 51.8 Mb and a scaffold N50 of 636.7 Mb. We anchored and oriented 99.7% of the assembly on seven pseudochromosomes and found that repetitive DNA sequences occupy 51.8% of the genome. Draft genome assemblies of three related species in the subfamily Phascogalinae, two additional antechinus species (A. argentus and A. arktos) and the iteroparous sister species Murexia melanurus were also generated. Preliminary demographic analysis supports the hypothesis that climate change during the Pleistocene isolated species in Phascogalinae and shaped their population size. A transcriptomic profile across the A. flavipes breeding season allowed us to identify genes associated with aspects of the male die-off. The chromosome-level A. flavipes genome provides a steppingstone to understanding an enigmatic life-history strategy and a resource to assist the conservation of antechinuses.

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Section: Genome Assembly and Annotationmentioning

confidence: 92%

Section: Repeat Element Annotationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A chromosome-level genome of Antechinus flavipes provides a reference for an Australasian marsupial genus with suicidal reproduction

Tian¹,

Han²,

Geng³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…This metric is an important contributing factor to the quality of 10x linked-read assemblies, with shorter molecules associated with reduced scaffold N50 and mis-assembly [41]. The antechinus genome had a molecule length of 74.08kb [40], compared to only 23.13kb for the numbat genome and below the recommended range of 50-100kb by 10x Genomics [41]. HMW DNA >40kb was used as input to sequencing in both species, although different extraction methods and kits were used in both cases which may have contributed to the difference in molecule length [40].…”

Section: Genomementioning

confidence: 99%

“…The antechinus genome had a molecule length of 74.08kb [40], compared to only 23.13kb for the numbat genome and below the recommended range of 50-100kb by 10x Genomics [41]. HMW DNA >40kb was used as input to sequencing in both species, although different extraction methods and kits were used in both cases which may have contributed to the difference in molecule length [40]. In addition, the numbat HMW DNA may have degraded during transport, storage, or sequencing, leading to fragmentation.…”

Section: Genomementioning

confidence: 99%

Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial

Peel

Silver

Brandies

et al. 2022

Preprint

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The numbat (Myrmecobius fasciatus) is a critically endangered Australian marsupial, and the last surviving member of the Myrmecobiidae family. The numbat regularly undergoes torpor and is unique amongst marsupials as it is the only diurnal and termitivorous species. Here we sequenced the first draft genome of the numbat using 10x Genomics chromium linked-read technology, resulting in a 3.42 Gbp genome with a scaffold N50 of 223 Kbp. A global transcriptome from liver, lung and tongue was also generated to aid genome annotation with Fgenesh++, identifying 21,465 protein-coding genes and 78.7% complete mammalian BUSCOs. To investigate adaptation to the numbat′s termitivorous diet and arid/semi-arid range, we interrogated the most highly expressed transcripts within the tongue and manually annotated taste, vomeronasal and aquaporin gene families. Antimicrobial proteins and proteins involved in digestion were highly expressed in the tongue, as expected. Similarly, umami taste receptors were also expressed in the tongue, however sweet taste receptors were not expressed in this tissue. This pattern of taste receptor expression, combined with the putative contraction of the bitter taste receptor gene repertoire in the numbat genome, may indicate a potential evolutionary adaptation to their specialized termitivorous diet. Vomeronasal and aquaporin gene repertoires were similar to other marsupials and have not undergone expansion or contraction. The draft numbat genome is a valuable tool for conservation and can be applied to population genetics/genomics studies and to investigate the unique biology of this interesting species.

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Threatened Species Initiative: Empowering conservation action using genomic resources

Hogg

Ottewell²,

Latch

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.

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The firstAntechinusreference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies

Cited by 8 publications

References 92 publications

A chromosome-level genome of Antechinus flavipes provides a reference for an Australasian marsupial genus with suicidal reproduction

A chromosome-level genome of Antechinus flavipes provides a reference for an Australasian marsupial genus with suicidal reproduction

Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial

Threatened Species Initiative: Empowering conservation action using genomic resources

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