Chromosome assembly and preliminary gene and repeat annotations for Myzomela tristrami reference genome

Secondary contact between closely related taxa represents a “moment of truth” for speciation — an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family — Myzomela cardinalis and Myzomela tristrami — carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome.

Methods
This data repository contains Myzomela tristrami reference genome files. The sequences associated with this assembly are available on NCBI sequence read archive at https://www.ncbi.nlm.nih.gov/sra/?term=SRA%20SRR29254783. We sequenced a M. tristrami female at the University of Delaware DNA sequencing & Genotyping Cener. HiFi libraries were prepared with SMRTbell prep kit, followed by Blue Pippin size selection (15-20Kbp) before sequencing on a PacBio Sequel IIe. We generated a de novo assembly using hifiasm v0.13-r308 with default parameters using the resulting long reads (Cheng et al. 2021, 2022). We used GeMoMa (v1.8) and the annotation from zebra finch genome bTaeGut1.4.pri to infer a rough annotation of genes in the Myzomela genome. We then used these rough annotations, comparing contigs against both zebra finch and the chicken genome bGalGal1.mat.broiler.GRCg7b to infer synteny relationships, remove duplicate haplotigs, and, finally, scaffold contigs into chromosomes in Myzomela. The resulting assembly uses the zebra finch numbering system for chromosomes 1-29; chromosome 30-40 were named in descending order of size. Final chromosomes and contigs were aligned with those of related species— helmeted honeyeater (Lichenostomus melanops cassidix), and blue-faced honeyeater (Entomyzon cyanotis)— using Mauve (version 2015-02-25), and visualized using FastANI (v1.33) (Darling et al. 2004, Jain et al. 2018, Robledo-Ruiz et al. 2022, Burley et al. 2023). We generated repetitive DNA libraries using the RepeatModeler v2 pipeline (Flynn et al. 2020). RepeatModeler employs a combination of de novo and homology-based characterization of different classes of repeats. The repeat library was annotated and combined with Repbase, and manually curated repeat libraries from other studies (Suh et al. 2018, Boman et al. 2019, Weissensteiner et al. 2020, Peona et al. 2021). We then used RepeatMasker ( v4.1.0) to identify and mask repetitive regions of the genome (Smit et al. 2013).

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