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. 2020 Mar 24;9(3):61. doi: 10.3390/biology9030061

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© 2020 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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Phylogeny of MYB TFs associated with the secondary metabolic pathway. Multiple sequence alignment of full-length amino acid is carried out using MAFFT 7.0 software (https://mafft.cbrc.jp/alignment/software/) with default parameters. The best substitution model of all amino acid sequences is determined by ModelFinder, and VT+F+R9 is found as the best model fit for these proteins. Maximum likelihood (ML) phylogenetic analysis is performed using IQ-tree software (http://www.iqtree.org/) with an SH-aLRT test for 1000 random addition replicates and a bootstrap test for 10,000 replicates [33,34]. The Figtree software (http://tree.bio.ed.ac.uk/software/figtree/) and iTOL (Interactive Tree of Life) website are used to visualize the phylogenetic trees [35]. The human protein c-MYB is used as an outgroup. The subfamilies (S1–S28) are designated as previously published papers. Accession numbers in DDBJ/EMBL/NCBI databases are as follows: LAP1 (ACN79541); MtPAR (ADU78729); LlMYB1 (ADY38393); LhMYB6 (BAJ05399); LhMYB12 (BAJ05398); LhMYB12-Lat (BAO04194); LjTT2a (BAG12893); LjTT2b (BAG12894); LjTT2c (BAG12895); C1 (AAA33482); PL (AAA19820); PL-BH (AAA33492); P1 (ABM21535); ZmMYB31 (NP_001105949); ZmMYB42 (ADX60106); ZmMYB-IF35 (AAO48737); GmMYB10 (ACM62751); PpMYB10 (ABX79945); CsRUBY (AFB73913); OgMYB1 (ABS58501); PcMYB10 (ABX71487); PyMYB10 (ADN26574); AN2 (AAF66727); DPL (ADW94950); PHZ (ADW94951); PhMYB27 (AHX24372); PtMYB1 (AAQ62541); PtMYB4 (AAQ62540); PtMYB134 (ACR83705); PtrMYB3 (AGT02395); PtrMYB20 (AGT02396); PttMYB21a (CAD98761); PtMYB134 (ACR83705); PtoMYB216 (AFI80906); StAN1 (AGC31676); StAN2 (AAX53089); StMTF1 (ABY40370); TaMYB14 (AEG64799); AmMYB308 (P81393); AmMYB330 (P81395); ROSEA1 (ABB83826); ROSEA2 (ABB83827); VENOSA (ABB83828); Y1 (AAX44239); GmMYB12B2 (AEC13303); GmMYB-G20-1 (BAK24100); FaMYB1 (AAK84064); FaMYB9 (AFL02460); FaMYB10 (ABX79947); FaMYB11 (AFL02461); PvMYB4a (AEM17348); NtAN2 (ACO52470); LeANT1 (AAQ55181); FtMYB1 (AEC32973); FtMYB2 (AEC32975); FtMYB13 (KY290579); FtMYB14 (KY290580); FtMYB15 (KY290581); FtMYB16 (KY290582); SbMYB8 (KF008657); TaPL1 (AK358937); SmMYB39 (KC213793); GbMYB5 (KY703716); GbMYB26 (KY703737); GbMYB31 (KY703742); GbMYBFL (KY678611); PgMYB2 (API61854.1); GtMYBP3 (AB733016); GtMYBP4 (AB289446); c-MYB (X52125).