Fig. 4: Analysis of LTR-RTs in P. australis genomes. | Communications Biology

Fig. 4: Analysis of LTR-RTs in P. australis genomes.

From: Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis

Fig. 4

a Insertion times of LTR-RTs in eight genomes, including two P. australis subgenomes. b Insertion times of significant types of P. australis LTR-RTs. The right panel indicates the significant types of LTR-RT insertion times for subgenome A and subgenome B, respectively. Pink and yellow shading indicate new and old transposon insertion events, respectively. c, d Evolutionary trees constructed from transposon sequences generated in new and old transposon insertion events in the Copia (c) and Gypsy (d) families. Evolutionary trees were constructed based on the complete reverse transcriptase structural domain sequences in the LTR-RTs sequences and visualised using ggtree (R package). The LTR-RT sequences are distinguished by different colours in the phylogenetic tree; further details can be found in the treefile (https://doi.org/10.6084/m9.figshare.27016279). e Normal QQ plot of Copia family content versus genome size for the P. australis genome. The normal distribution test using the Shapiro-Wilk (SW) method. f Pearson correlation analysis between Copia family content and genome size in the P. australis genome. g Differences in transposon content between two sets of subgenes in P. australis.

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