This is a final project for the Comparative Genomics seminar in the spring of 2019. The main goal of this project is production of a high quality annotation of the recently sequenced Portulaca amilis genome. Secondary goals include characterizing gene family expansion of key photosynthetic genes (e.g. PEPC) and comparing our geneome, in general, and these gene families, in particular, to other C3, C4, and CAM taxa.
.fasta
.fasta
.fasta
.csv
For a step-by-step walkthrough, refer to the wiki. Here is a brief outline of the methodology.
QUAST
, gVolante
, and BUSCO
Trinity
Transdecoder
with Beta vulgaris and Arabidopsis thaliana proteomesRepeatModeler
and masked with RepeatMasker
MAKER
SNAP
and Augustus
MAKER
and ab initio gene predictionThe main result of the project is itself the annotated genome, which is currently a work in progress. At this time I have finished the initial annotation, trained gene model predictors, and begun reannotating using these predictors. Along the way I have recorded a number of important statistics about the size, completeness, and content of the P. amilis genome.
Size distribution
Total length (nt) | 403885173 |
---|---|
Longest sequence (nt) | 53436919 |
Shortest sequence (nt) | 1000 |
Mean sequence length (nt) | 99651 |
Median sequence length (nt) | 1476 |
N50 sequence length (nt) | 42597560 |
L50 sequence count | 5 |
Number of sequences > 1K (nt) | 4046 (99.8% of total number) |
Number of sequences > 10K (nt) | 32 (0.8% of total number) |
Number of sequences > 100K (nt) | 13 (0.3% of total number) |
Number of sequences > 1M (nt) | 9 (0.2% of total number) |
Number of sequences > 10M (nt) | 9 (0.2% of total number) |
Sum length of sequences > 1M (nt) | 395389203 (97.9% of total length) |
Sum length of sequences > 10M (nt) | 395389203 (97.9% of total length) |
Genome completeness
My first annotation with MAKER
recovered a large fraction of those found in the raw scaffolds. I expected that the number of duplicated genes would be higher in this annotation because we retained isoforms for many gene from the transcriptome analysis during annotation.
BUSCO | Initial MAKER |
Input scaffolds |
---|---|---|
Complete BUSCOs | 1031 (71.6%) | 1291 (89.7%) |
Complete and single-copy BUSCOs | 814 (56.5%) | 1228 (85.3%) |
Complete and duplicated BUSCOs | 217 (15.1%) | 63 (4.4%) |
Fragmented BUSCOs | 158 (11.0%) | 29 (2.0%) |
Missing BUSCOs | 251 (17.4%) | 120 (8.33%) |
Total BUSCO groups searched | 1440 | 1440 |
I also combined some data on genome size and completeness from Zhao and Schranz (2019) to see how our assembly compares to other angiosperm assemblies. The P. amilis genome is among the highest quality (at least in terms of N50 and BUSCO) of publically available angiosperm genomes.
Genome content
After the initial MAKER
analysis I recovered 23,893 predicted genes with a mean length of 3,661.38 bp. I estimated the genome to be constituted of ~46% repetitive elements.
The next computational steps in annotating the Portulaca amilis genome include
MAKER
circos
) and gene models with a genome browserfunannotate
with some additional/updated methodology
PASA
In addition to expanding my computational methodology, I am also in the process of generating more molecular data to bolster our annotation. In particular, I am generating transcriptomes from multiple tissue types of P. amilis under normal environmental conditions that should increase the completeness of our genome annotation. I am also generating long-read transcriptomes for normal and drought-stressed leaves, to understand the full diversity of photosynthesis-related transcripts.