Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence

Abstract

Accurate feature annotation as well as assembly contiguity are important requisites of a modern genome assembly. They allow large-scale comparison of genomes across and within species and identification of polymorphisms, leading evolutionary and functional studies. We report an updated genome resource for Metrosideros polymorpha, the most dominant tree species in the Hawaiian native forests and a unique example of rapid and remarkable ecological diversification of woody species. Ninety-one percent of the bases in the sequence assembly (304 Mb) were organized into 11 pseudo-molecules, which would represent the chromosome structure of the species assuming the synteny to a close relative Eucalyptus. Our complementary approach using manual annotation and automated pipelines identified 11.30% of the assembly to be transposable elements, in contrast to 4.1% in previous automated annotation. By increasing transcript and protein sequence data, we predicted 27,620 gene models with high concordance from the supplied evidence. We believe that this assembly, improved for contiguity, and annotation will be valuable for future evolutionary studies of M. polymorpha and closely related species, facilitating the isolation of specific genes and the investigation of genome-wide polymorphisms associated with ecological divergence.

Evolution of glucuronoxylan side chain variability in vascular plants and the counter-adaptation of pathogenic cell-wall-degrading hydrolases

“…For the XAPT phylogeny, XAPT orthologues from a wide range of tracheophyte species were extracted from our recent phylogeny of GT47-A enzymes (Yu et al ., 2022), which contained protein sequences from Plaza Dicots 4.5, Plaza Monocots 4.5, and Plaza Gymnosperms 1.0 (Van Bel et al ., 2018), as well as from several independent genomes. To obtain further XAPT orthologues from plants in the Myrtales order, the genomes of Metrosideros polymorpha (Izuno et al, 2016; Izuno et al, 2019), Rhodamnia argantea , Syzygium oleosum , and Punica granatum (all available from NCBI Genome, https://www.ncbi.nlm.nih.gov/genome/) and the transcriptome of Oenothera rosea (Carpenter et al, 2019; One Thousand Plant Transcriptomes, 2019), were searched using TBLASTN (Altschul et al ., 1990) using At XAPT1 as a query with a cut-off at E = 1 × 10 -125 . Sequences were aligned using MUSCLE (Edgar, 2004a; Edgar, 2004b) and truncated to the GT47 domain.…”

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

“…After trimming adapter sequences and low-quality bases using Trimmomatic (ver. 0.33) [75], the clean reads were aligned against the M. polymorpha reference genome sequence [22] using the BWA-MEM algorithm (ver. 0.7.12-r1039) [76].…”

“…For variant sites, SNPs with more than three alleles were excluded from the dataset and the effect of SNPs on gene functions were estimated using SnpEff (ver. 4.3T) [78] based on the M. polymorpha gene annotation [22]. A total of 243,376,950 sites, including 231,298,492 monomorphic sites and 12,078,458 bi-allelic SNPs, were used for subsequent analyses.…”

“…newelii [16]. With the aid of a genome assembly composed of chromosomescale pseudo-molecules [22], we investigated the whole-genome polymorphisms of 70 samples from 55 localities covering the altitudinal range, lava types, and five varieties from across the island. Firstly, we examined the population structure of M. polymorpha on the island and identified the primary evolutionary units that are genetically differentiated along environmental gradients across the island.…”

Selection on old variants drives adaptive radiation ofMetrosiderosacross the Hawaiian Islands

“…We used the MAKER program (Cantarel et al 2008) for gene annotation using the workflow outlined on the website https://gist.github.com/darencard/bb1001ac1532dd4225b030cf0cd61ce2. The transcriptome assembly from stringtie2 was used as EST evidence in MAKER, and the protein sequences from the previous M. polymorpha assembly (Izuno et al 2019), E. grandis assembly (Myburg et al 2014), and A. thaliana (TAIR10) were used for a protein homology search in MAKER. After an initial round of MAKER annotation the gene models were used by SNAP (Korf 2004) and Augustus (Stanke et al 2008) to create gene model training datasets specifically for our M. polymorpha genome assembly.…”