| Analysis Name | Saccharum spontaneum Np-X Assembly & Annotation |
| Sequencing technology | Illumina; PacBio |
| Assembly method | Canu v. 1.9 |
| Release Date | 2022-03-04 |
Zhang Q, Qi Y, Pan H, Tang H, Wang G, Hua X, Wang Y, Lin L, Li Z, Li Y, Yu F, Yu Z, Huang Y, Wang T, Ma P, Dou M, Sun Z, Wang Y, Wang H, Zhang X, Yao W, Wang Y, Liu X, Wang M, Wang J, Deng Z, Xu J, Yang Q, Liu Z, Chen B, Zhang M, Ming R, Zhang J. Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. Nat Genet. 2022 Jun;54(6):885-896. doi: 10.1038/s41588-022-01084-1.
AbstractSaccharum spontaneum is a founding Saccharum species and exhibits wide variation in ploidy levels. We have assembled a high-quality autopolyploid genome of S. spontaneum Np-X (2n = 4x = 40) into 40 pseudochromosomes across 10 homologous groups, that better elucidates recent chromosome reduction and polyploidization that occurred circa 1.5 million years ago (Mya). One paleo-duplicated chromosomal pair in Saccharum, NpChr5 and NpChr8, underwent fission followed by fusion accompanied by centromeric split around 0.80 Mya. We inferred that Np-X, with x = 10, most likely represents the ancestral karyotype, from which x = 9 and x = 8 evolved. Resequencing of 102 S. spontaneum accessions revealed that S. spontaneum originated in northern India from an x = 10 ancestor, which then radiated into four major groups across the Indian subcontinent, China, and Southeast Asia. Our study suggests new directions for accelerating sugarcane improvement and expands our knowledge of the evolution of autopolyploids.
Assembly statistics
| Genome size | 2.8 Gb |
| Total ungapped length | 2.8 Gb |
| Number of chromosomes | 40 |
| Number of scaffolds | 1,033 |
| Scaffold N50 | 68.6 Mb |
| Scaffold L50 | 17 |
| Number of contigs | 15,510 |
| Contig N50 | 381.9 kb |
| Contig L50 | 2,133 |
| GC percent | 44.5 |
| Genome coverage | 18.0x |
| Assembly level | Chromosome |
The Saccharum spontaneum Np-X Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Saccharum_spontaneum_NpX.assembly.fna.gz |
The Saccharum spontaneum Np-X genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Saccharum_spontaneum_NpX.gff3.gz |
| CDS sequences (FASTA file) | Saccharum_spontaneum_NpX.cds.fna.gz |
| Protein sequences (FASTA file) | Saccharum_spontaneum_NpX.protein.faa.gz |
Functional annotation for the Saccharum spontaneum Np-X is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Saccharum_spontaneum.Pfam.tsv.gz |
Summary
| Query | Chromosome | Size(bp) | Coordinates | tBLASTn Hit | tBLASTn %ID | Domain |
| DUF247I-S1 | Chr10A | 62086223 | 36843964-36845649 | Shybrid | 70 | DUF247 |
| DUF247I-S2 | Chr10B | 62776581 | 35239746-35241422 | Shybrid | 67 | DUF247 |
| DUF247I-S3 | Chr10C | 59107536 | 35474463-35476151 | Shybrid | 66 | DUF247 |
| DUF247I-S4 | Chr10C | 59107536 | 35391752-35393440 | Shybrid | 66 | DUF247 |
| DUF247I-S5 | Chr10D | 59917352 | 33271657-33273345 | Shybrid | 71 | DUF247 |
| DUF247II-S1 | Chr10A | 62086223 | 36638159-36639805 | Shybrid | 64 | DUF247 |
| DUF247II-S2 | Chr10B | 62776581 | 34555297-34556922 | Shybrid | 60 | DUF247 |
| DUF247II-S3 | Chr10C | 59107536 | 34185050-34186663 | Shybrid | 61 | DUF247 |
| DUF247II-S4 | Chr10D | 59917352 | 32758250-32759872 | Shybrid | 61 | DUF247 |
| HPS10-S1 | Chr10A | 62086223 | 36642060-36642163,36642249-36642414 | ShybridS1 | 73 | - |
| HPS10-S2 | Chr10B | 62776581 | 34559513-34559619,34559697-34559859 | ShybridS1 | 58 | - |
| HPS10-S3 | Chr10C | 59107536 | 34188680-34188842,34188964-34189073 | ShybridS1 | 54 | - |
| HPS10-S4 | Chr10C | 59107536 | 34213383-34213492,34213614-34213776 | ShybridS1 | 54 | - |
| HPS10-S5 | Chr10D | 59917352 | 33844600-33844759,33844908-33845020 | ShybridS1 | 67 | - |
| DUF247I-Z1 | Chr6A | 57781833 | 51728058-51729647 | Shybrid | 62 | DUF247 |
| DUF247I-Z2 | Chr6B | 59431965 | 50372017-50373600 | Shybrid | 62 | DUF247 |
| DUF247I-Z3 | Chr6C | 64971179 | 58793187-58794812 | Shybrid | 58 | DUF247 |
| DUF247I-Z4 | Chr6D | 60951635 | 55855053-55856756 | Shybrid | 61 | DUF247 |
| DUF247II-Z1 | Chr6A | 57781833 | 51776753-51778411 | Shybrid | 50 | DUF247 |
| DUF247II-Z2 | Chr6B | 59431965 | 50248865-50250505 | Shybrid | 53 | DUF247 |
| DUF247II-Z3 | Chr6C | 64971179 | 58806801-58808447 | Shybrid | 49 | DUF247 |
| DUF247II-Z4 | Chr6D | 60951635 | 55869760-55871466 | Shybrid | 50 | DUF247 |
| HPS10-Z1 | Chr6A | 57781833 | 51764237-51764393,51764465-51764574 | ShybridZ5 | 42 | - |
| HPS10-Z2 | Chr6B | 59431965 | 50259004-50259110,50259208-50259367 | ShybridZ6 | 56 | - |
| HPS10-Z3 | Chr6C | 64971179 | 58804978-58805146,58805242-58805354 | Scereale | 64 | - |
| HPS10-Z4 | Chr6D | 60951635 | 55868527-55868680,55868792-55868880 | ShybridZ5 | 35 | - |
Nucleotide
Protein