MSc project: Assembly, annotation and analysis of the long-tailed finch genome

There is growing interest in applying genomic approaches to the study of non-model species. Genomic approaches can offer insight into questions of adaptation, speciation, and population genetics. For example, genomic resources and tools can help reveal the genetic basis of reproductive isolation between diverging lineages and help understand the genetic background of phenotypic traits under selection in natural populations.

Birds are one of the most highly successful and diverse groups of vertebrates, characterised by a number of characteristic features, such as feathers, wings, and hollow bones. Birds also exhibit the smallest and least variable genome sizes among tetrapods; genome size estimates reveal a range of only approximately two-fold (approx. 1-2 pg or roughly 1-2 billion bases).

The long-tailed finch (Poephila acuticauda, family Estrildidae) is a small passerine bird endemic to Australia. Two sub-species are recognised differentiated by bill colour – yellow in the western subspecies acuticauda and red in the eastern subspecies hecki. These subspecies diverged approximately 0.3 mya, but have more recently come into secondary contact (approx. 14-21 kya). Currently, the subspecies overlap in a narrow zone where hybridization occurs and hybrid individuals exhibit intermediately coloured bills. However, admixture is generally limited and there is evidence that selection acts against hybrids and/or parentals and thus maintains the sub-species as independently evolving populations. More recent evidence suggests the emergence of reproductive isolation in this system may be due to mitonuclear/sex chromosome incompatibilities. Thus, the long-tailed finch system offers a window into the genetic architecture of reproductive isolation in a young system. Currently, however, we lack a well annotated genome to inform future studies.

In this project, you will assemble and annotate the genome for the long-tailed finch using Illumina 10X data, PacBio HiFi data, and Illumina RNASeq data. The core tasks will be: (1) researching approaches to genome assembly and annotation, (2) structural annotation of the long-tailed finch genome using the selected tools, and (3) functional annotation of the transcriptome using BREAKER. Optional tasks may include investigation of copy number variation in the long-tailed finch genome compared to that of the closely related zebra finch, investigation and generation of gene trees of genes related to bill colouration, or investigation of immunity genes putatively linked to reproductive isolation. Alternatively, we welcome project ideas from the student.

Your profile 

• Highly motivated. Candidate with interest in evolutionary biology and genomics 
• Experience in Advanced bioinformatics, Genomics, Genome analysis, Python desirable
• English skills as English is the language of the project team.