Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree.

Orzenil Bonfim Silva-Junior,Evandro Novaes,Dario Grattapaglia,Rosane G Collevatti

doi:10.1093/gigascience/gix125

Orzenil Bonfim Silva-Junior, Evandro Novaes + Show 2 more

Open Access

https://doi.org/10.1093/gigascience/gix125

Copy DOI

Abstract

Background Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica. Regarded as the “new mahogany,” it is the second most expensive timber, the most logged species in Brazil, and currently under significant illegal trading pressure. The plant produces large amounts of quinoids, specialized metabolites with documented antitumorous and antibiotic effects. The development of genomic resources is needed to better understand and conserve the diversity of the species, to empower forensic identification of the origin of timber, and to identify genes for important metabolic compounds.FindingsThe genome assembly covers 503.7 Mb (N50 = 81 316 bp), 90.4% of the 557-Mbp genome, with 13 206 scaffolds. A repeat database with 1508 sequences was developed, allowing masking of ∼31% of the assembly. Depth of coverage indicated that consensus determination adequately removed haplotypes assembled separately due to the extensive heterozygosity of the species. Automatic gene prediction provided 31 688 structures and 35 479 messenger RNA transcripts, while external evidence supported a well-curated set of 28 603 high-confidence models (90% of total). Finally, we used the genomic sequence and the comprehensive gene content annotation to identify genes related to the production of specialized metabolites.ConclusionsThis genome assembly is the first well-curated resource for a Neotropical forest tree and the first one for a member of the Bignoniaceae family, opening exceptional opportunities to empower molecular, phytochemical, and breeding studies. This work should inspire the development of similar genomic resources for the largely neglected forest trees of the mega-diverse tropical biomes.

Highlights

Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica
This work should inspire the development of similar genomic resources for the largely neglected forest trees of the mega-diverse tropical biomes
We considered as heterozygous redundant those scaffolds that showed pairwise similarity to exactly another sequence, and their depth of coverage fell in a Poisson distribution with parameters given by the heterozygous peak of the read depth distribution over all scaffolds (Fig. 2B)

Summary

Introduction

Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica. After gene model prediction and refinements, a total of 36 262 gene models were found in the genome assembly, and 31 668 of them were retained after quality assessment based on Cscore, protein coverage, and overlap with repeats, as described in the “Methods.” The number of predicted messenger RNA (mRNA) transcripts was 35 479.

Results

Conclusion