Extended Data Fig. 9: Molecular evolutionary analyses of S-ELF3. | Nature Plants

Extended Data Fig. 9: Molecular evolutionary analyses of S-ELF3.

From: Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat

Extended Data Fig. 9: Molecular evolutionary analyses of S-ELF3.The alternative text for this image may have been generated using AI.

a, Maximum likelihood phylogenetic tree based on the amino acid sequences of the homologues of S-ELF3 and putative evolutionary scenario of S-ELF3. Sequences of S-ELF3 are from a previously study11 under the following GenBank accessions numbers - AB641416 (F. esculentum S-ELF3), AB641417 (F. cymosum S-ELF3), and AB641418 (F. urophyllum S-ELF3). Sources of the remaining sequences are as described in Supplementary Table 19. Alignment was performed using MAFFT with the option -linsi and filtered with trimAl with the options ‘-automated1 -resoverlap 0.7 -seqoverlap 50’. Phylogenetic tree was constructed using the resulting alignments as input with IQ-TREE with 1,000 bootstrap replicates. The tree was rooted using the two Arabidopsis genes and FesPL4_sc0096.1.g000180.1 as outgroup. The F. tataricum ortholog of FesPL4_r1.1_Chr5.g038430.1 (FtPinG0006101400.01.T01) was filtered out as the result of trimAl. Bootstrap values of ≥80% are indicated next to each node. The magenta dot corresponds to a whole-genome duplication. G and IS encode for style length and style incompatibility, respectively. b,Ks between the S-ELF3 genes in F. esculentum, F. cymosum, F. urophyllum, and the paralogs in F. esculentum. Ks was calculated using codeml of the PAML package. The Ks estimates between FesPL4_sc0096.1.g000180.1 and the other FagopyrumS-ELF3 homologues are > 3 and not shown.

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