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Table 1 Evidence supporting extensive gene duplication in cat fleas

From: A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity

Approach

Source

Key points

Genome size estimation

Fig. 2a, Fig S2

- C. felis from two populations have the same mean genome size.

- Individual cat fleas vary ~ 118 Mb in estimated genome size.

- Individual rat fleas vary ~ 100 Mb in estimated genome size.

Long-read assembly with proximity ligation

Fig. 1, Fig. S1, Table S5

- Nine scaffolds > 10 Mb are littered with gene duplications, which comprise 38% of protein-coding genes.

- No misassembly of allelic variants in the BIG9 scaffolds.

Transcript mapping

Fig. 2d

- 98% of duplicate genes have transcriptional support in RNA-Seq data from an independent colony (1KITE).

Short-read mapping

Fig. 2c

- Short-read data map with far greater depth to single-copy genes versus duplicate genes.

Assessment of duplication lengths

Fig. 2e

- 69% of duplications are divergent in length; heterogeneity in length and composition are positively correlated.