Supplemental Material for Brose et al., 2020

<i>Mitragyna speciosa</i> Korth., 1839 (kratom) produces numerous compounds with pharmaceutical properties including the production of bioactive monoterpene indole and oxindole alkaloids. Using a linked-read approach, a 1,122,519,462 bp draft assembly of <i>M. speciosa</i> ‘Rifat’ was generated with an N50 scaffold size of 1,020,971 bp and an N50 contig size of 70,448 bp that encodes 55,746 genes. Chromosome counting revealed that Rifat is a tetraploid with a base chromosome number of 11, which was further corroborated by orthology and syntenic analysis of the genome. Analysis of genes and clusters involved in specialized metabolism revealed genes putatively involved in alkaloid biosynthesis. Access to the genome of <i>M. speciosa</i> will facilitate an improved understanding of alkaloid biosynthesis and accelerate production of bioactive alkaloids in heterologous hosts.Figure S1 contains the scaffold mean read depth distributions in the final assembly. Figure S2 contains the frequency of gene counts in orthogroups between Rubiaceae species. Table S1 is a list of RNA-Seq, WGS, and 10X Chromium Libraries. Table S2 contains a list of chloroplast genomes used to identify sequences encoding the chloroplast genome in <i>Mitragyna speciosa. </i>Table S3 contains metrics of quality assessments based on alignment of whole genome shotgun sequencing to the final <i>Mitragyna speciosa</i> 'Rifat' assembly. Table S4 contains metrics of quality assessments based on alignment of RNA sequencing to the final <i>Mitragyna speciosa </i>'Rifat' assembly. Table S5 the Repeat Masker summary of results of elements in the <i>Mitragyna speciosa </i>genome. Table S6 contains the FPKM expression matrix of top five blast results of <i>Mitragyna speciosa</i> 'Rifat' working set of genes and<i> Catharanthus roseus</i>. Table S7 contains predicted biosynthetic clusters in <i>Mitragyna speciosa</i>.<br>