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 con..., 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 Myzomel..., , # Chromosome assembly and preliminary gene and repeat annotations for Myzomela tristrami reference genome
I. Files
(GENOME)
Mt_v1.0_MAIN.fa.gz
Primary genome, (largely) scaffolded to chromosome-level, plus other primary assembled contigs
Mt_v1.0_MAIN.gff.gz
Simple gene annotations for primary genome, annotated using GeMoMa v1.8 and a zebra finch
(bTaeGut1.4.pri) annotation reference
Mt_v1.0_extra.fa.gz
Additional contigs, not for use in most analyses but some may be of interest
This set is a combination of hand-identified haplotigs of the main genome, and assembler-identified
\"alternate\" (haplotig) contigs
(ORIGINAL_ASSEMBLY_CONTIGS)
Mt_hifi.asm.p.fa.gz
\"primary\" assembly contigs, output from hifiasm (v0.13-r308)
Mt_hifi.asm.a.fa.gz
\"alternate\" assembly contigs, output from hifiasm (v0.13-r308)
(REPEAT_MASKING)
TElib_Myzo_preliminary.fa.gz
Preliminary Myzomela-tuned TE/repeat library, generated using RepeatModeler (v.2)
Mt_v1.0_MAIN_RM_sites_to_filter.txt
List of sites masked by RepeatM...