Fig. 3: Expansion and contraction of gene families. | Nature Communications

Fig. 3: Expansion and contraction of gene families.

From: Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Fig. 3

a Phylogenetic tree based on single-copy genes from nine lepidopteran species. Fam (+/−) represents the number of expansion and contraction of gene families in eight butterfly species. RPLP0, RPLP1 and RPLP2 represent the number of each family in eight butterfly species. b 433 processed pseudogenes originated from one complete RPLP2 gene in P. glacialis. c The intron number of 433 processed pseudogenes in P. glacialis. d Coverage length of 433 processed pseudogenes in P. glacialis. Coverage length is the ratio between the length of translated pseudogene and the length of one complete RPLP2 protein in P. glacialis. e Comparison of Ka/Ks rates between inter-species and intra species for RPLP2 genes (n = 9 and 374, left to right, respectively). The Ka/Ks rates of inter-species were calculated based on the complete RPLP2 genes of P. glacialis (Pglac-RPLP2) and other eight lepidopteran species. The Ka/Ks rates of intra-species were calculated based on one complete RPLP2 gene (Pglac-RPLP2) and 433 processed pseudogenes in P. glacialis (Among them, 374 pseudogenes were calculated the valid Ka/Ks rates with Pglac-RPLP2). For box plots, center lines show the medians; box bounds stand for the 25th and 75th percentiles; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles. Source data was shown in the source data file (Fig. 3e). f The RNA expressions of 433 processed pseudogenes at different altitudes in P. glacialis. BQTM and BQXL stand for the low- and high- populations. g Venn of specific processed pseudogenes with normal expression (log2(TPM + 1) ≥ 1) in the low- and high-altitude populations (BQTM and BQXL) for P. glacialis.

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