Whole-Genome Assembly of the maize NAM founders

About this project

Maize is not only an important crop but an important study species for answering basic questions about how plants grow and adapt to different environments. Genome assemblies, which are complete representations of the genetic information in a plant variety, are critical resources for answering these important questions. However, currently only a single type specimen is used as the sequence reference for most of the genetic information in maize, leaving unknown much of the highly valuable natural variation in maize. This project will assemble the genomes of 26 additional maize lines, chosen to represent a broad cross section of the maize lines used in modern breeding. The sequence assemblies will be enhanced by adding information about the nature of the genes and how the genomes differ from each other. All information will be released on an accelerated schedule through public databases.

Deliverables

All genomes (including PacBio long reads, Illumina reads, optical maps, scaffolds, and AGP files) are uploaded to EBI and will be released on publication or January, 2020, whichever comes first. B73 Ab10 (BioProject ID PRJEB35367) will only be released after publication. Links will be active on Jan 9th, 2020.

1. Raw datasets (PacBio, BioNano, Illumina and RNASeq) and Genome Assemblies

• For all 25 NAM assemblies: BioProject ID PRJEB31061 and ArrayExpress ID (RNASeq) E-MTAB-8633 .

• For B73 version 5: BioProject ID PRJEB32225 and ArrayExpress ID (RNASeq) E-MTAB-8628.

• For EM-seq data (methylation) ArrayExpress ID E-MTAB-10088.

• For ATAC-seq data NCBI-GEO ID GSE165787.

2. Genome Assembly and Annotations

• MaizeGDB FTP site for bulk download.

• CyVerse download via iRods (public folder: /iplant/home/shared/NAM/NAM_genome_and_annotation_Jan2021_release). Details on how to use iRods for bulk download can be found here.

• MaizeGDB genome browser.

3. Other information

• MaizeGDB NAM metadata and general information link.

• Scripts and protocols (in progress) GitHub.

Maize Meeting 2021 talk presented by Prof. Kelly Dawe

Publications

Journal Articles

1. Ou, S., Su, W., Liao, Y., Chougule, K., Ware, D., Peterson, T., Jiang, N., Hirsch, C.N. and Hufford, M.B. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol 20, 275 (2019) doi:10.1186/s13059-019-1905-y
2. Hufnagel, D.E., M.B. Hufford, A.S. Seetharam. SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. BMC Bioinformatics 21, 429 (2020). 10.1186/s12859-020-03751-8
3. Manchanda, N., Portwood, J.L., Woodhouse, M.R., Seetharam, A.S., Lawrence-Dill, C.J., Andorf, C.M. and Hufford, M.B., GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations. BMC Genomics 21, 193 (2020). doi: 10.1186/s12864-020-6568-2
4. Ou, S., Liu, J., Chougule, K.M., Fungtammasan, A., Seetharam, A., Stein, J., Llaca, V., Manchanda, N., Gilbert, A.M., Wei, X. and Chin, C.S. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nat Commun 11, 2288 (2020). doi: 10.1038/s41467-020-16037-7
5. Liu, J., Seetharam, A., Chougule, K., Ou, S., Swentowsky, K., Gent, J., Llaca, V., Woodhouse, M., Manchanda, N., Presting, G., Kudrna, D., Alabady, M., Hirsch, C., Fengler, K., Ware, D., Michael, T., Hufford, and M., Dawe, K. Gapless assembly of maize chromosomes using long-read technologies. Genome Biol 21, 121 (2020). doi: 10.1186/s13059-020-02029-9
6. Hufford, M.B., Seetharam, A.S., Woodhouse, M.R., Chougule, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Coletta, R.D., Tittes, S., Hudson, A.I., Marand, A.P., Wei, S., Lu, Z., Wang, B., Ruiz, M.K.T., Piri, R.D., Wang, N., Kim, D.K., Zeng, Y., O'Connor, C.H., Li, X., Gilbert, A.M., Baggs, E., Krasileva, K.V., II, J.L.P., Cannon, E.KS., Andorf, C.M., Manchanda, N., Snodgrass, S.J., Hufnagel, D.E., Jiang, Q., Pedersen, S., Syring, M.L., Kudrna, D.A., Llaca, V., Fengler, K., Schmitz, R.J., Ross-Ibarra, J., Yu, J., Gent, J.I., Hirsch, C.N., Ware, D., Dawe, R.K. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv 2021.01.14.426684 (2021). doi: 10.1101/2021.01.14.426684

Press Releases

• NSF award page
• Pacific Biosciences Press Release, July 10, 2018
• ISU Press Release, Jan 17, 2018
• Maize Collaborators Embark on Ambitious 26-line Pangenome Project
• UGA to lead NSF project to rapidly sequence corn pangenome