Convergent molecular evolution among ash species resistant to the emerald ash borer

Abstract

Recent studies show that molecular convergence plays an unexpectedly common role in the evolution of convergent phenotypes. We exploited this phenomenon to find candidate loci underlying resistance to the emerald ash borer (EAB; Agrilus planipennis ), the USA’s most costly invasive forest insect to date, within the pan-genome of ash trees (the genus Fraxinus ). We show that EAB-resistant taxa occur within three independent phylogenetic lineages. In genomes from these resistant lineages, we detect 53 genes with evidence of convergent amino acid evolution. Gene tree reconstruction indicates that for 48 of these candidates, the convergent amino acids are more likely to have arisen via independent evolution than by another process, such as hybridisation or incomplete lineage sorting. Seven of the candidate genes have putative roles connected to the phenylpropanoid biosynthesis pathway and 17 relate to herbivore recognition, defence signalling or programmed cell death. Evidence for loss-of-function mutations among these candidates is more frequent in susceptible species, than in resistant ones. Our results on evolutionary relationships, variability in resistance, and candidate genes for defence response within the ash genus could inform breeding for EAB resistance, facilitating ecological restoration in areas this beetle has invaded.

Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes

“…We gathered molecular information from several genomic compartments (chloroplastic, mitochondrial and nuclear) for 61 Oleaceae species representative of all currently recognized tribes, subtribes and genera in Oleaceae. Both plastid and mitochondrial DNA datasets as well as the nrDNA cluster are based on relatively high sequencing depth (>30×) and thus of a high quality [30,41]. In contrast, low-copy nuclear genes are more difficult to assemble from genome skimming data and their use in phylogenetics is still a challenge due to lower coverage and recurrent whole genome duplications [31,48].…”

“…Recent developments in genomics and museomics present new opportunities to tackle such obstacles, though. Several Oleaceae nuclear and cytoplasmic genomes, as well as transcriptomes have been released [31,[38][39][40][41][42][43]. Also herbarium samples, previously deemed unusable, are now accessible allowing for a more comprehensive sampling, and the inclusion of rare, or recently extinct species [31,[44][45][46].…”

Global challenges facing plant pathology: multidisciplinary approaches to meet the food security and environmental challenges in the mid-twenty-first century

“…Although genetic markers for selection and breeding are routinely made available, can resistance be developed in time to manage emerging and invasive threats such as by targeting generic stress-response mechanisms (Newton et al 2012)? The challenges in plant breeding are especially striking when considering tree crops which have slow growth and a long generation time (Boshier and Buggs 2015;Kelly et al 2020;Showalter et al 2020;Stocks et al 2017). In these cases, the evaluation of the durability or resistance traits will take several decades.…”

Metabolic and Transcriptional Profiling of Fraxinus chinensis var. rhynchophylla Unravels Possible Constitutive Resistance against Agrilus planipennis

“…rhynchophylla compared with F. pennsylvanic. Additionally, one DEG (FRAX09_000207320), which might be involved in the transport of the JA precursor 2-oxophytodienoic acid (OPDA) from the chloroplast [37], and EIN3, which mediates JA and ET signaling synergy [24], showed greater levels, suggesting their constitutive enhancement of the JA and ET pathways and the synergy between the two pathways in F. chinensis var. rhynchophylla.…”

“…Finally, a total of 49810040, 51728718, 56054150, 59228236, 52148240, and 45870910 clean reads were obtained in the R1, R2, R3, S1, S2, and S3 libraries, respectively, with Q30 values ≥ 93.56%. The genome Version 0.2 assembly and Version 0.2 annotation of F. pennsylvanica (accession PE_00248) [37] were downloaded from http://www.ashgenome.org (accessed on 5 June 2021) and used as reference. The alignment of the paired-end reads to the reference was performed using the HISAT2 software [47].…”