Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids

Abstract

<jats:title>Abstract</jats:title> <jats:p>Chiococca alba (L.) Hitchc. (snowberry), a member of the Rubiaceae, has been used as a folk remedy for a range of health issues including inflammation and rheumatism and produces a wealth of specialized metabolites including terpenes, alkaloids, and flavonoids. We generated a 558 Mb draft genome assembly for snowberry which encodes 28,707 high confidence genes. Comparative analyses with other angiosperm genomes revealed enrichment in snowberry of lineage-specific genes involved in specialized metabolism. Synteny between snowberry and Coffea canepehora Pierre ex A. Froehner (coffee) was evident, including the chromosomal region encoding caffeine biosynthesis in coffee, albeit syntelogs of N-methyltransferase were absent in snowberry. A total of 27 putative terpene synthase genes were identified, including 10 that encode diterpene synthases. Functional validation of a subset of putative terpene synthases revealed that combinations of diterpene synthases yielded access to products of both general and specialized metabolism. Specifically, we identified plausible intermediates in the biosynthesis of merilactone and ribenone, structurally unique antimicrobial diterpene natural products. Access to the C. alba genome will enable additional characterization of biosynthetic pathways responsible for health-promoting compounds in this medicinal species.</jats:p>

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

“…Bosser [ 29 ] . The plastid genome from short-reads of C. pubescens had a length of 156,985 base pairs (bp) and a GC content of 37.74%, very similar to other Rubiaceae plastid genomes [ 25 , 30 ] . Lastly, we demonstrate the utility and reliability of our resources by constructing nuclear and plastid phylogenomic frameworks of C. pubescens .…”

“…The assemblies were generated using a combination of extensive long-read Oxford Nanopore (∼218×) and short-read Illumina paired-end read datasets (∼300×) jointly with state-of-the-art genome assemblers. This resulted in a reference genome for which contiguity and quality are comparable to, or even higher [ 25 ] than in the five published genome assemblies in Rubiaceae available at the time of submission of this study, namely for Chiococca alba (L.) Hitch. [ 25 ] , Coffea canephora Pierre ex A. Froehner [ 26 ] , Coffea arabica L. [ 27 ] , Mitragyna speciosa Korth.…”

“…This resulted in a reference genome for which contiguity and quality are comparable to, or even higher [ 25 ] than in the five published genome assemblies in Rubiaceae available at the time of submission of this study, namely for Chiococca alba (L.) Hitch. [ 25 ] , Coffea canephora Pierre ex A. Froehner [ 26 ] , Coffea arabica L. [ 27 ] , Mitragyna speciosa Korth. [ 28 ] and Neolamarckia cadamba (Roxb.)…”

A highly contiguous, scaffold-level nuclear genome assembly for the Fever tree (Cinchona pubescens Vahl) as a novel resource for research in the Rubiaceae

“…Here, we present the first high-quality draft nuclear and plastid genomes of C. pubescens , which is characterised by having a genome size of 1.1 Gb (1C, this study) and a chromosome number of 2 n =34. The assemblies were generated using a combination of extensive long-read Nanopore (∼218x) and short-read Illumina paired-end read datasets (∼300x) jointly with state-of-the-art genome assemblers, resulting in a reference genome for which contiguity and quality are comparable to, or even higher [22] than in the three previously published genome assemblies in Rubiaceae, namely for Chiococca alba [22], Coffea canephora [23], and Coffea arabica [24] . The plastid genome from short-reads of C. pubescens had a length of 156,985 bp and a GC content of 37.74%, very similar to other Rubiaceae plastid genomes [22,25].…”

“…The assemblies were generated using a combination of extensive long-read Nanopore (∼218x) and short-read Illumina paired-end read datasets (∼300x) jointly with state-of-the-art genome assemblers, resulting in a reference genome for which contiguity and quality are comparable to, or even higher [22] than in the three previously published genome assemblies in Rubiaceae, namely for Chiococca alba [22], Coffea canephora [23], and Coffea arabica [24] . The plastid genome from short-reads of C. pubescens had a length of 156,985 bp and a GC content of 37.74%, very similar to other Rubiaceae plastid genomes [22,25]. Lastly, we demonstrate the utility and reliability of our resources by constructing nuclear and plastid phylogenomic frameworks of C. pubescens .…”