De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin

Abstract

Camptotheca acuminata is 1 of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. While transcriptome studies have been performed previously with various camptothecin-producing species, no genome sequence for a camptothecin-producing species is available to date. We generated a high-quality de novo genome assembly for C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50 scaffold size of 1752 kbp. Quality assessments of the assembly revealed robust representation of the genome sequence including genic regions. Using a novel genome annotation method, we annotated 31 825 genes encoding 40 332 gene models. Based on sequence identity and orthology with validated genes from Catharanthus roseus as well as Pfam searches, we identified candidate orthologs for genes potentially involved in camptothecin biosynthesis. Extensive gene duplication including tandem duplication was widespread in the C. acuminata genome, with 2571 genes belonging to 997 tandem duplicated gene clusters. To our knowledge, this is the first genome sequence for a camptothecin-producing species, and access to the C. acuminata genome will permit not only discovery of genes encoding the camptothecin biosynthetic pathway but also reagents that can be used for heterologous expression of camptothecin and camptothecin analogs with novel pharmaceutical applications.

Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North AmericanNyssa(Nyssaceae)

“…ursina using Bowtie2 and SAMtools to obtain the consensus sequence for each locus per sample. The sequences of three additional samples were obtained from other databases (Table 1), including one N. sinensis (transcriptome data) and two outgroups, Camptotheca acuminata (genome data from Zhao et al, 2017) and Davidia involucrata (transcriptome data from Li et al, 2016). Sequence data for N. yunnanensis were recovered from Hyb-seq of genes captured from the Angiosperm 353 probes by Rapid Genomics (Gainesville, Florida), and the orthologs of N. yunnanensis were obtained through the pipeline of HybPiper (Johnson et al, 2016).…”

Genomic analyses of a “living fossil”: The endangered dove‐tree

“…We employed augustus (version 3.2.3) (Stanke & Morgenstern, 2005) for de novo annotation. We used proteins of apple (Malus domestica) (Daccord et al, 2017), Arabidopsis thaliana (Cheng et al, 2017), Eucalyptus grandis (Myburg et al, 2014), soybean (Glycine max) (Schmutz et al, 2010), Camptotheca acuminata (Zhao et al, 2017) and Populus trichocarpa (Tuskan et al, 2006) for homologous prediction by genewise (Birney, Clamp, & Durbin, 2004). All gene models were integrated using evidencemodeler (version 1.1.1) (Haas et al, 2008) to obtain a consensus gene set.…”

“…We identified orthologous and paralogous groups using the annotated genes and the other eight species, A. thaliana (Cheng et al, 2017), Camptotheca acuminata (Zhao et al, 2017), Catharanthus roseus (Kellner et al, 2015), Coffea canephora (Denoeud et al, 2014), Daucus carota (Cai et al, 2015), Lactuca sativa (Verwaaijen et al, 2018), Rhododendron delavayi (Zhang et al, 2017) and Vitis vinifera (Jaillon et al, 2007) by orthomcl (version 2.0.9) (Li, Stoeckert, & Roos, 2003) and mmseqs (Hauser, Steinegger, & Söding, 2016) with an e-value threshold of 1e-5. Subsequently, we selected 1,971 single-copy orthogroups and constructed phylogenetic relationships between these species.…”

Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis

“…The MIAs comprise approximately 3000 compounds, with chemical scaffolds so different that it is not always obvious that the chemicals are biosynthetically related . This enormous chemical complexity stands in contrast to only three sequenced MIA producers, namely Catharanthus roseus (Apocynaceae, order Gentianales), Rhazya stricta (Apocynaceae, order Gentianales) and Camptotheca acuminata (Nyssaceae, order Cornales) . Only a small number of the genes accounting for the enormous diversity of MIAs are known so far, and these are primarily from C. roseus .…”