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Genome Sequencing Project Information |
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Project name |
The sequencing and assembly of the 26 maize Nested Association Mapping (NAM) founder lines |
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GenBank BioProject |
PRJEB31061 |
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Project PI |
Kelly Dawe |
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Project start date |
2018-01-01 |
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Contributors |
Kelly Dawe, Doreen Ware, Matthew Hufford, Kevin Fengler, Candice Hirsch, Kapeel Chougle, Arun Seetharam, Michael Syring, Marcella K. Tello-Ruiz, Sharin Wei, Margaret Woodhouse, Jonathan Gent, Shujun Ou, David Hufnagel, Jianing Liu, Nancy Manchanda, Sarah Pedersen, Samantha Snodgrass |
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Funding |
Whole genome assembly of the maize NAM founders NSF Award #1744001 |
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Publication status |
published |
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Project reference |
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.
Hufford MB, Seetharam AS, Woodhouse MHR, Chougule KM, Ou S, Liu JN, Ricci WA, Guo TT, Olson AC, Qiu YJ, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu ZY, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng YB, O'Connor CH, Li XR, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang QH, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler KA, Schmitz RJ, Ross-Ibarra J, Yu JM, Gent JI, Hirsch CN, Ware DH, Dawe RK
At MaizeGDB
PMID
DOI
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Sequencing and Assembly Information |
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Assembly name |
Zm-NC350-REFERENCE-NAM-1.0 |
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Assembly date |
Spring 2019 |
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Assembly accession |
GCA_902167005 |
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WGS accession |
CABHKU010000000 |
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Assembly provider |
Corteva |
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Sequencing description |
Sequencing technologies: PacBio Sequencing method: SEQUEL Genome coverage: 66X |
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Assembly description |
Assembly methods: PacBio sequencing, CANU1.8 assembly, scaffolds validated by BioNano optical mapping, and ordered and oriented using linkage data Construction of pseudomolecules: Pseudomolecules were constructed from superscaffolds using genetic maps; gap sizes are 100N |
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Browse Genome |
Genome browser at MaizeGDB |
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Data download |
https://download.maizegdb.org/Zm-NC350-REFERENCE-NAM-1.0 ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/all_assembly_versions/GCA_902167005.1_Zm-NC350-REFERENCE-NAM-1.0
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Finishing strategy |
complete genome |
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Assembly statistics |
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Scaff num |
1,399 |
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Total scaff length |
2,290,501,892 bp |
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Longest scaff |
200,526,522 bp |
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Shortest scaff |
30,309 bp |
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N50 scaff length |
100,662,410 bp |
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Total number of scaffolds in assembly.
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Total sequence length represented by scaffolds.
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Longest scaffold in assembly.
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Shortest scaffold in assembly.
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The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
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A contig is a contiguous consensus sequence that is
derived from a collection of overlapping reads.
A scaffold is set of a ordered and orientated contigs
that are linked to one another by mate pairs of sequencing reads.
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