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

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.

Using molecular markers to investigate genetic diversity, mating system and gene flow of Neotropical trees

“…However, phylogeography studies have also made use of markers such as SSRs and SNPs because they are more useful for detecting gene flow or genetic structure between intra-specific populations. In addition, in the last eight years the technique of NGS (Next Generation Sequencing) has been applied to tree species (see Mccormack et al 2013), and recently the first assembly of a neotropical tree species genome was carried out (Pink Ipe, Silva-Junior et al 2018).…”

Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome

“…The first one targeted transcript sequences of protein-coding genes predicted from the genome assembly of H. impetiginosus UFG-1. 27 These probes were designed by RAPiD Genomics LLC, Gainesville, FL, USA, from a total of 17,424 transcript sequences, which were tiled with 26,526 120-mer DNA sequence probes. The second set, designed by our group, sampled SNPs identified in pooled low coverage WGS data.…”

“…We used nearly 20 Gbp of data (70,049,993 pairs of reads) for the SNP calling process. From the empirically determined haploid genome size of 557 Mbp/1C for H. impetiginosus , 27 this read set corresponded to nearly 3× of sequencing coverage in the pool of 12 chromosomes. Based on the 23,508 variants derived from the GATK 28 and the 9,079 from the Cortex 29 analysis, the genome assembly of the species was used as a template for the design of 120-mer probes surrounding the SNP vicinity.…”

“…Sequencing reads were trimmed for adapters and aligned to a genome sequence assembly of H. impetiginosus 27 with BWA 30 version 0.5.9 using BWA-backtrack algorithm, default settings. These steps were performed in a grid computing cluster software system using a pipeline available from the International Cassava Genetic Map Consortium.…”

“…We have recently generated a preliminary genome assembly and annotation of the nuclear genome sequence of a single individual of H. impetiginosus . 27 Using these resources as reference, in this work we designed and carried out an evaluation of a set of 30,795 sequence capture probes for the identification and genotyping of nearly 200,000 SNPs located inside circa of 14,000 annotated protein-coding genes or in close proximity to them to support multiple sequence-based genetic analyses in the species.…”