Supporting Information Tables S1–S2 and Figures S1–S5:

Table S1 Primers for qRT-PCR

Table S2 List of Auxin/indoleacetic acid genes

Figure S1 The frequency distribution of transcript and unigenes

Figure S2Histogram of the KOG classification cluster of C. orbiculatus sequences

Figure S3 Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched pathways identified the function of unigenes

FigureS4 Clusters of differentially expressed genes during the aril developmentGreen indicates a decrease in transcript abundance, and red means increase.

Figure S5 The expression patterns of MADS genesCO-F2:full-blooming stage; CO-F3: flower senescence after fertilization stage; CO-YF1: young fruit stage.

Gene ID / Forward primer（5’-3’） / Reverse primer（5’-3’） / length(bp) / Ta(℃)
c43219_g1 / AAACACCAATTCCCACTCCA / ATAGGTAAGAGAAGGGCAATG / 103 / 60
c41380_g2 / ATCAAGAGAGCTTCATCCAC / AAGCCGTTTAGGGATTGT / 133 / 60
c40128_g2 / AAATCATGGAGGAGATCACTG / CTGCCCTTTCCCATTAGTT / 110 / 60
c43365_g3 / GCTAAGTGTGAAGTGTGATCT / AACTGCTTTGTTCTCCCT / 144 / 60
c37713_g1 / TAGGTCTGGGTCTGTGTTT / GCTACCAGGAATTGAGCG / 100 / 60
c6895_g1 / GGAGAACAGCCAAGTAGT / AGATTGGGATCTTGAAGGTTAG / 104 / 60
c39346_g1 / AGCATCACACAGAACAGT / AGGAGCAGAAGAGAAACG / 183 / 60
c40128_g1 / TAAGGATAGAAGATTTGCGGC / CGTTCTCTTCCATCAATAACAT / 138 / 60

TableS1 Primers for qRT-PCR

TableS2 List of Auxin/indoleacetic acid genes

uinigene ID / Genename / fpkm(CO_F2) / fpkm(CO_F3) / fpkm(CO_YF1) / length / NR Description
c42598_g1 / IAA9 / 332.15 / 326.89 / 459.74 / 1848 / hypothetical protein JCGZ_15935
c28821_g1 / IAA16 / 128.43 / 130.36 / 104.61 / 1164 / Indoleacetic acid-induced protein 16
c65990_g1 / AUX22B / 58.54 / 46.33 / 62.06 / 1428 / unnamed protein product
c44139_g1 / At3g48380 / 56.86 / 64.28 / 64.34 / 6044 / PREDICTED: uncharacterized protein LOC102613560
c27955_g2 / ARF8 / 40.02 / 30.68 / 55.98 / 522 / PREDICTED: auxin response factor 8-like isoform 1
c27854_g1 / IAA29 / 36.56 / 22.24 / 39.63 / 1455 / hypothetical protein PRUPE_ppa010871mg
c21700_g1 / ARF23 / 36.35 / 43.67 / 101.38 / 987 / PREDICTED: auxin response factor 2-like
c35085_g3 / AUX28 / 31.39 / 31.36 / 7.19 / 653 / auxin-induced protein aux28
c44139_g2 / IAA26 / 22.15 / 22.26 / 20.87 / 2002 / hypothetical protein JCGZ_24854
c39631_g2 / IAA11 / 21.14 / 22.61 / 40.15 / 1051 / Auxin-responsive protein IAA13, putative
c43492_g1 / ARF4 / 11.53 / 11.55 / 26.86 / 4787 / hypothetical protein JCGZ_05557
c16890_g1 / AUX22D / 10.99 / 7.64 / 39.53 / 499 / PREDICTED: auxin-induced protein 22D
c41311_g1 / IAA26 / 9.78 / 12.7 / 43.65 / 1705 / PREDICTED: auxin-responsive protein IAA26, partial
c24540_g1 / IAA20 / 9.1 / 8.8 / 5.65 / 861 / hypothetical protein JCGZ_14120
c30394_g1 / IAA30 / 8.56 / 4.2 / 25.32 / 466 / Auxin-responsive protein IAA27, putative
c43167_g1 / PXL2 / 7.52 / 8.89 / 6.57 / 4352 / leucine-rich repeat transmembrane protein kinase
c31820_g1 / IAA8 / 6.22 / 6.59 / 31.1 / 985 / hypothetical protein JCGZ_06321
c23231_g1 / IAA14 / 6 / 1.07 / 3.38 / 421 / hypothetical protein JCGZ_02272
c40204_g1 / IAA13 / 5.71 / 4.43 / 12.38 / 1790 / Auxin-responsive protein IAA13, putative
c9670_g1 / IAA7 / 3.03 / 0 / 6.06 / 211 / PREDICTED: auxin-responsive protein IAA14
c36721_g1 / IAA27 / 2.07 / 1.72 / 7.05 / 1132 / unnamed protein product
c13550_g1 / IAA18 / 1.29 / 1.27 / 6.4 / 433 / hypothetical protein PRUPE_ppa013361mg
c24106_g1 / IAA10 / 1.28 / 1.09 / 2.95 / 470 / hypothetical protein POPTR_0006s06550g
c43008_g2 / ARF18 / 1.07 / 2.61 / 8.11 / 535 / Auxin response factor, putative
c19636_g1 / AUX22 / 0.67 / 0.44 / 24.06 / 468 / unknown
c61927_g1 / ARF24 / 0.58 / 0.38 / 0.36 / 511 / hypothetical protein CICLE_v10019257mg

Figure S1. The frequency distribution of transcript and unigenes

Figure S2. Histogram of the KOG classification cluster of C. orbiculatus sequences

Figure S3. Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched pathways identified the function of unigenes

FigureS4. Clusters of differentially expressed genes during the aril developmentGreen indicates a decrease in transcript abundance, and red means increase.

Figure S5. The expression patterns of MADS genesCO-F2:full-blooming stage; CO-F3: flower senescence after fertilization stage; CO-YF1: young fruit stage