Chromosomal-scale assembly of the liverwort Marchantia paleacea
Issa (University of Zurich, Switzerland) opened the presentation by describing Marchantia paleacea as ‘a flagship model of plant evolution’, having an ‘incredible dual system of reproduction’, and rapid growth – from spore to adult plant within 3 weeks. Further advantages of this plant as a model organism include its haploid-dominant life cycle, a relatively small genome size at ~230-280 Mb, and ease of genetic manipulation. Next, Issa turned to the importance of DNA quality and purity for sequencing, recommending >0.5 μg of DNA, a Nanopdrop/Qubit ratio of >2, and A260/280 of 1.8-2.0, and an A260/230 of 2.0-2.2. For purification, the team utilise either CTAB without shearing, or bead-based purification with g-TUBE shearing. Sequencing for this project was performed using the Ligation Sequencing Kit (LSK109) and the GridION device.
The data provided 64X genome coverage across 277 contigs with an N50 of 2.2 Mb. Genome assembly was assessed using three assemblers: Miniasm, Tulip, and wtdbg2; with all tools yielding an assembly of the estimated genome size. Comparing their genome against the reference genome for M. polymorpha, which had been generated using short-read sequencing technology, revealed very high homology between the species; however, due to the use of long nanopore sequencing reads, the M. paleacea assembly comprised half as many contigs. Issa described how the team then performed Hi-C scaffolding to generate a chromosomal-scale assembly, resolving all 8 autosomes.
In the final section of the talk, Issa spoke about their work annotating the genome and examining gene synteny with M. polymorpha. They discovered that the M. paleacea genome exhibits a higher proportion of unique genes (with higher copy numbers), some of which, they believe, may be involved in endosymbiosis, which is absent in M. polymorpha.