Alignment statistics to assess the read content of the transcriptome of R. arboreum

Read type Count PercentageProper pairs 49,766,521 81.35Improper pairs 4,802,224 7.85Left only 3,354,400 5.48Right only 3,254,304 5.32Total aligned RNA-Seq fragments 61,177,449

A distribution characteristic of the percent length coverage for the top matching Swiss-Prot database hit

Length coverage bin (%)Count of database proteins in bin

Cumulative count of database proteins >/= bin level

100 7,138 7,13890 2,018 9,15680 1,339 10,49570 1,193 11,68860 1,243 12,93150 1,261 14,19240 1,319 15,51130 1,294 16,80520 803 17,60810 150 17,758

A summary of completeness of R. arboreum transcriptome as per the comparison with BUSCOs from plant lineage dataset

Feature StatsComplete BUSCOs 1193Complete and single copy BUSCOs 874Complete and duplicated BUSCOs 319Fragmented BUSCOs 95Missing BUSCOs 152Total BUSCO groups searched 1440

Major species represented by GO terms of the annotated transcripts in R. arboreum

A summary of KEGG pathway annotations

Pathway # unigenes # enzymesRibosome 390 128Spliceosome 328 103Carbon metabolism 325 92Biosynthesis of amino acids 287 98Protein processing in endoplasmic reticulum 286 76Plant-pathogen interaction 280 34Plant hormone signal transduction 235 40RNA transport 209 97Starch and sucrose metabolism 189 33Purine metabolism 188 86Endocytosis 180 57Oxidative phosphorylation 178 81mRNA surveillance pathway 165 50Ubiquitin mediated proteolysis 156 56Glycolysis / Gluconeogenesis 154 31RNA degradation 151 50Pyrimidine metabolism 146 73Amino sugar and nucleotide sugar metabolism 142 38Phenylpropanoid biosynthesis 117 18Glutathione metabolism 115 17Ribosome biogenesis in eukaryotes 115 56Phagosome 113 29Photosynthesis 113 38Peroxisome 112 37Glycerophospholipid metabolism 109 36Glyoxylate and dicarboxylate metabolism 101 28Pyruvate metabolism 98 31Cysteine and methionine metabolism 91 32Glycine, serine and threonine metabolism 91 33Carbon fixation in photosynthetic organisms 90 25Glycerolipid metabolism 85 24Nucleotide excision repair 85 37Arginine and proline metabolism 81 24Fatty acid metabolism 80 28Insulin resistance 78 14N-Glycan biosynthesis 76 31Aminoacyl-tRNA biosynthesis 74 26Basal transcription factors 73 30Base excision repair 71 27Pentose and glucuronate interconversions 71 14Proteasome 68 35Phosphatidylinositol signaling system 67 21Protein export 67 26Fructose and mannose metabolism 66 20DNA replication 65 32Citrate cycle (TCA cycle) 63 19Regulation of autophagy 63 15Galactose metabolism 62 16Inositol phosphate metabolism 62 24Pentose phosphate pathway 62 16Terpenoid backbone biosynthesis 62 29Valine, leucine and isoleucine degradation 62 202-Oxocarboxylic acid metabolism 61 28beta-Alanine metabolism 61 16Homologous recombination 61 27Phenylalanine, tyrosine and tryptophan biosynthesis 61 22Porphyrin and chlorophyll metabolism 58 31SNARE interactions in vesicular transport 57 18RNA polymerase 56 29Alanine, aspartate and glutamate metabolism 55 27

Ascorbate and aldarate metabolism 55 16Fatty acid degradation 52 11Mismatch repair 51 21Circadian rhythm - plant 48 19Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 47 22Tyrosine metabolism 47 18alpha-Linolenic acid metabolism 44 13Ubiquinone and other terpenoid-quinone biosynthesis 44 20Phenylalanine metabolism 43 15Sphingolipid metabolism 43 15Arginine biosynthesis 42 21Fatty acid biosynthesis 41 15Sulfur metabolism 41 14Histidine metabolism 40 11Cyanoamino acid metabolism 39 9Lysine degradation 39 10Biosynthesis of unsaturated fatty acids 37 12Propanoate metabolism 37 14Tryptophan metabolism 37 9Flavonoid biosynthesis 35 15Folate biosynthesis 35 11Nitrogen metabolism 33 12Carotenoid biosynthesis 32 16One carbon pool by folate 32 10Pantothenate and CoA biosynthesis 31 17Fatty acid elongation 30 7Photosynthesis - antenna proteins 29 12Steroid biosynthesis 29 17Ether lipid metabolism 27 7Nicotinate and nicotinamide metabolism 25 13Other glycan degradation 23 9Isoquinoline alkaloid biosynthesis 21 9Riboflavin metabolism 21 6Selenocompound metabolism 21 9Arachidonic acid metabolism 20 7Brassinosteroid biosynthesis 19 7Tropane, piperidine and pyridine alkaloid biosynthesis 19 8Vitamin B6 metabolism 19 8Zeatin biosynthesis 19 6Flavone and flavonol biosynthesis 18 5ABC transporters 17 6Biotin metabolism 17 8Cutin, suberine and wax biosynthesis 16 8Lysine biosynthesis 16 9Thiamine metabolism 16 7Butanoate metabolism 15 10Diterpenoid biosynthesis 15 9Glycosaminoglycan degradation 15 5Limonene and pinene degradation 15 2Stilbenoid, diarylheptanoid and gingerol biosynthesis 15 5Valine, leucine and isoleucine biosynthesis 14 10Monobactam biosynthesis 13 6Other types of O-glycan biosynthesis 13 5Other types of O-glycan biosynthesis 13 5Sulfur relay system 13 9Glycosphingolipid biosynthesis - globo series 12 3Linoleic acid metabolism 12 3Monoterpenoid biosynthesis 12 4Monoterpenoid biosynthesis 12 4Sesquiterpenoid and triterpenoid biosynthesis 12 6Taurine and hypotaurine metabolism 12 3Betalain biosynthesis 10 2Non-homologous end-joining 10 8

Degradation of aromatic compounds 9 3Glucosinolate biosynthesis 7 2Isoflavonoid biosynthesis 7 2Lipoic acid metabolism 7 2Anthocyanin biosynthesis 6 3Butirosin and neomycin biosynthesis 6 1C5-Branched dibasic acid metabolism 6 5Tetracycline biosynthesis 6 4D-Glutamine and D-glutamate metabolism 5 1Synthesis and degradation of ketone bodies 5 3Glycosphingolipid biosynthesis - ganglio series 4 2Biosynthesis of ansamycins 3 1Caffeine metabolism 3 2Aflatoxin biosynthesis 1 1Biosynthesis of siderophore group nonribosomal peptides 1 1Polyketide sugar unit biosynthesis 1 1Vancomycin resistance 1 1

A summary of proportion of the 59 different TF families in transcriptome of R. arboreum

TF_Family # Unique Peptides # Unique TFs

bHLH 2,186 290NAC 1,465 167MYB-related 1,377 194WRKY 1,263 155FAR1 1,149 169B3 1,071 114MYB 947 166C2H2 904 202C3H 903 180bZIP 850 140ERF 771 156G2-like 648 96GRAS 538 86HD-ZIP 448 77S1Fa-like 394 14M-type 370 39Nin-like 338 83TALE 332 32HSF 326 46GATA 314 67HB-other 301 52TCP 297 41NF-YB 289 29MIKC 281 47Trihelix 273 57YABBY 265 15LBD 260 49E2F/DP 246 28BES1 217 29Dof 199 43GeBP 197 25NF-YA 188 18ARF 178 50SBP 172 41CAMTA 144 31AP2 140 32NF-YC 137 20WOX 129 9CO-like 97 21DBB 92 12STAT 85 9ARR-B 83 40ZF-HD 79 12NF-X1 72 11EIL 66 8CPP 65 13GRF 53 21RAV 47 8BBR-BPC 41 10SRS 38 6VOZ 37 3LSD 31 9HRT-like 22 6HB_PHD 17 5Whirly 7 3LFY 3 2SAP 3 2NB-other 2 1NZZ/SPL 1 1

Amplification profile generated for the loci, namely (A.) F4_c142711_g1_i1, and (B.) F4_c20375_g1_i1). Lanes 1- 30 represent sampled individuals of R. arboreum; Ld: 100 bp DNA ladder (Bangalore GeneiTM) as size standard