Maize Reference Assemblies for Satellite Evolution Analysis

We created 13 genome assemblies of maize and teosinte for a comparative analysis of satellite DNA evolution using PacBio HiFi data.

For each assembly, high-confidence HiFi contigs were generated using HiFiasm (v 0.19.6) with homozygous settings with end-joining disabled (--write-ec --write-paf -u0 -l0). High confidence contigs (>1/2 expected read depth) were then scaffolded using the T2T Mo17 assembly (Chen et al., 2023 https://doi.org/10.1038/s41588-023-01419-6) using RagTag (v2.0.1) (Alonge et al., 2023 https://doi.org/10.1186/s13059-022-02823-7). Scaffolded assemblies were annotated with Liftoff (v1.6.3) twice, once using gene annotations from Mo17 T2T as the reference and once using the gapless B73 AB10 as reference (Liu et al., 2020 https://doi.org/10.1186/s13059-020-02029-9 ). Assemblies contain only chromosomes.

The B73 AB10 assembly was generated using the same high molecular weight DNA used in a prior publication (Liu et al., 2020 https://doi.org/10.1186/s13059-020-02029-9 ). HiFi reads accessible via NCBI [INSERT REFERENCE NUMBER]

The B73 assembly was generated using reads from SRR11606869 (Hon et al., 2020 https://doi.org/10.1038/s41597-020-00743-4).

The Mo17 assembly was generated using from reads from PRJNA751841 (Chen et al., 2023 https://doi.org/10.1038/s41588-023-01419-6).

CG44, CG119, CG108, Tx777, and Tx779 assemblies were generated using reads from PRJEB59044. These genomes were sequenced as part of the Genomes to Fields Project, with seeds sourced from the Germplasm Resources Information Network (GRIN).

K64 and CML44 assemblies were generated fusing reads from PRJEB66502 collected from the Buckler lab at Cornell University and funded by the Bill and Melinda Gates Foundation. 

TIL01, TIL11, and TIL25 were generated using reads from  PanAnd data (PRJEB50280).