Genome Reference Assembly for Bottlenecked Southern Australian Koalas

Abstract

Koala populations show marked differences in inbreeding levels and in the presence or absence of the endogenous Koala Retrovirus (KoRV). These genetic differences among populations may lead to severe disease impacts threatening koala population viability. In addition, the recent colonization of the koala genome by KoRV provides a unique opportunity to study the process of retroviral adaptation to vertebrate genomes and the impact this has on speciation, genome structure and function. The genome build described here is from an animal from the bottlenecked “Southern” population free of endogenous and exogenous KoRV. It provides a more contiguous genome build than the previous koala reference derived from an animal from a more outbred “Northern” population and is the first koala genome from a KoRV polymerase free animal.

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)

“…Using a multi-pronged annotation approach of transcript and protein-level alignment, as well as ab initio gene prediction (Figure 2 ), we obtained 58,271 putative gene models for the fat-tailed dunnart draft genome (Table 4 ). Of these gene models, 21,622 were protein-coding (BLAST hits to UniProt/Swiss-Prot), which is in line with the reported gene numbers for the numbat (21,465) [ 55 ] , the koala (27,669) [ 106 ] , the Tasmanian devil (19,241) [ 43 ] , the brown antechinus (25,111) [ 53 ] , the tammar wallaby (15,290) [ 52 ] , and the gray short-tailed opossum (21,384) [ 51 ] (Table 5 ). Furthermore, we predicted the putative function of the fat-tailed dunnart proteins using several curated protein databases (Table 4 , Figure 3 ).…”

De novotranscriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)

“…Using a multi-pronged annotation approach of transcript and protein-level alignment, as well as ab initio gene prediction (Figure 3), we obtained 58,271 putative gene models for the fat-tailed dunnart draft genome (Table 3). Of these gene models, 21,622 were protein-coding (BLAST hits to UniProt/Swiss-Prot), which is in line with the reported gene numbers for the numbat (21,465) [58], the koala (27,669) [104], the Tasmanian devil (19,241) [46], the brown antechinus (25,111) [56], the tammar wallaby (15,290) [55], and the gray short-tailed opossum (21,384) [54] (Table 4). Furthermore, we predicted the putative function of the fat-tailed dunnart proteins using several curated protein databases (Table 3, Figure 3).…”

Contrasting segregation patterns among endogenous retroviruses across the koala population

“…The widely recognized, major genetic differentiation between northern (NSW and QLD) and southern (VIC and SA) koala populations has directed most population management in the past 15,16,27 . The main contributor to this differentiation is the effective extinction and subsequent reintroduction of koalas into the southern states from relict island populations during the early 20th century 16 . As a result, the southern states have very low genetic diversity on the SNP level [27][28][29] .…”

“…The phaCin-β-like integrations show no apparent pairwise structure across the koala population, consistent with a longer residence in the koala germline. Comparison of phaCin-β insertion polymorphism in koala genomes assemblies Recently, a second high-quality koala genome assembly became available 16 . The newly sequenced individual was from the bottlenecked South Australian (SA) population, allowing us to compare its phaCin-β ERV integrations to those of the reference koala assembly ("Bilbo"), which was from QLD.…”