Solanum pennellii acc. LA5240 / LYC1722
Recent updates in Oxford Nanopore technology (R9.4) have made it possible to obtain GBases of sequence data from a single flowcell. However, unlike other next generation sequencing technology, Oxford Nanopore based sequencing doesn’t require any a priori capital investments. We therefore evaluated whether Oxford Nanopore can be used to analyze plant genomes. To this aim, we sequenced and assembled the accession LA5240 (LYC1722) of the wild tomato species Solanum pennellii, an accession that was identified spuriously. Unlike the Solanum pennellii accession LA0716, for which we have previously generated a high quality draft genome, the accession LA5240 does not appear to exhibit any dwarfed, necrotic leaf phenotype when introgressed into modern tomato cultivars.
Here we present approximately 134 Gbases of third generation sequencing data representing a raw coverage of ca 110x. This corresponds to 110GBases of data passing the Oxford nanopores quality filter representing about 90x coverage. In addition we provide approximately 20-30x coverage of Illumina data. Average Q value represents a normal average of all Q values (as delivered in e.g. FastQC) in a read and is higher than the one reported by Oxford Nanopore.
Publication
Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Mass J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.
Plant Cell. 2017 Oct; 29(10): 2336-2348
Data
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genome assembly data from EBI
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Nanopore MinION sequencing data
FAST5 files | Fastq files (Metrichor v1.121) | Fastq files (Albacore 2.1.1) | Fastq (Metrichor v1.121) | Fastq (Albacore 2.1.1) | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
unfiltered | filtered | unfiltered | filtered | ||||||||||||||||||||
# reads | Yield | RL average | longest Read | avg. Q | # reads | Yield | RL average | longest Read | avg. Q | # reads | Yield | RL average | longest Read | avg. Q | # reads | Yield | %PF | RL average | longest Read | avg. Q | |||
20161027_Spenn_001_001 (512GB) | 20161027_Spenn_001_001 | 20161027_Spenn_001_001 | 252,424.00 | 3,339,142,817.00 | 13,228.00 | 258,042.00 | 8.96 | 205,010.00 | 2,818,546,677.00 | 13,748.00 | 71,457.00 | 9.55 | 252,980.00 | 3,502,241,408.00 | 13,843.95 | 390,285.00 | 8.95 | 222,992.00 | 3,210,123,159.00 | 0.92 | 14,395.69 | 76,034.00 | 9.46 |
20161101_Spenn_002_002 (826GB) | 20161101_Spenn_002_002 | 20161101_Spenn_002_002 | 439,240.00 | 5,183,715,529.00 | 11,802.00 | 171,384.00 | 8.79 | 340,880.00 | 4,202,561,007.00 | 12,329.00 | 81,554.00 | 9.49 | 439,296.00 | 5,461,248,451.00 | 12,431.82 | 170,901.00 | 8.68 | 365,518.00 | 4,755,062,637.00 | 0.87 | 13,009.11 | 170,901.00 | 9.34 |
20161103_Spenn_003_003 (1.1TB) | 20161103_Spenn_003_003 | 20161103_Spenn_003_003 | 520,761.00 | 6,650,042,702.00 | 12,770.00 | 160,531.00 | 8.87 | 412,111.00 | 5,466,343,110.00 | 13,264.00 | 95,933.00 | 9.43 | 521,334.00 | 6,962,701,269.00 | 13,355.55 | 166,463.00 | 8.72 | 443,147.00 | 6,193,529,874.00 | 0.89 | 13,976.24 | 166,463.00 | 9.32 |
20161108_Spenn_004_004 (753GB) | 20161108_Spenn_004_004 | 20161108_Spenn_004_004 | 431,400.00 | 5,252,529,782.00 | 12,176.00 | 147,621.00 | 8.86 | 343,999.00 | 4,360,721,187.00 | 12,677.00 | 105,470.00 | 9.45 | 431,474.00 | 5,540,797,850.00 | 12,841.56 | 140,235.00 | 8.82 | 371,673.00 | 4,973,407,918.00 | 0.90 | 13,381.14 | 140,235.00 | 9.37 |
20161108_Spenn_004_005 (1.1TB) | 20161108_Spenn_004_005 | 20161108_Spenn_004_005 | 561,300.00 | 7,058,376,081.00 | 12,575.00 | 206,494.00 | 8.95 | 458,908.00 | 6,009,783,868.00 | 13,096.00 | 92,999.00 | 9.46 | 561,362.00 | 7,428,206,310.00 | 13,232.47 | 233,377.00 | 8.87 | 491,757.00 | 6,795,726,493.00 | 0.91 | 13,819.28 | 233,377.00 | 9.38 |
20161110_Spenn_005_006 (813GB) | 20161110_Spenn_005_006 | 20161110_Spenn_005_006 | 380,518.00 | 5,364,783,960.00 | 14,099.00 | 190,799.00 | 8.83 | 298,794.00 | 4,460,813,385.00 | 14,929.00 | 131,801.00 | 9.44 | 380,705.00 | 5,653,369,695.00 | 14,849.74 | 138,150.00 | 8.71 | 322,980.00 | 5,104,296,304.00 | 0.90 | 15,803.75 | 138,150.00 | 9.38 |
20161110_Spenn_005_007 (732GB) | 20161110_Spenn_005_007 | 20161110_Spenn_005_007 | 346,686.00 | 4,956,793,607.00 | 14,297.00 | 164,918.00 | 9.07 | 285,832.00 | 4,294,311,690.00 | 15,023.00 | 109,564.00 | 9.55 | 347,079.00 | 5,218,433,504.00 | 15,035.29 | 143,906.00 | 8.92 | 304,640.00 | 4,824,584,280.00 | 0.92 | 15,837.00 | 143,906.00 | 9.47 |
20161112_Spenn_006_008 (431GB) | 20161112_Spenn_006_008 | 20161112_Spenn_006_008 | 219,392.00 | 2,942,797,165.00 | 13,413.00 | 131,281.00 | 9.10 | 176,739.00 | 2,535,756,222.00 | 14,347.00 | 89,450.00 | 9.63 | 219,571.00 | 3,077,195,783.00 | 14,014.58 | 123,787.00 | 8.86 | 185,767.00 | 2,800,253,293.00 | 0.91 | 15,074.01 | 89,970.00 | 9.59 |
20161112_Spenn_006_009 (732GB) | 20161112_Spenn_006_009 | 20161112_Spenn_006_009 | 379,071.00 | 5,171,422,068.00 | 13,642.00 | 149,605.00 | 9.07 | 313,732.00 | 4,464,764,479.00 | 14,231.00 | 100,221.00 | 9.55 | 379,237.00 | 5,448,867,688.00 | 14,367.97 | 132,020.00 | 9.00 | 334,238.00 | 5,009,007,328.00 | 0.92 | 14,986.35 | 105,329.00 | 9.49 |
20161114_Spenn_007_010 (1.1TB) | 20161114_Spenn_007_010 | 20161114_Spenn_007_010 | 451,070.00 | 6,721,699,609.00 | 14,901.00 | 198,894.00 | 8.74 | 344,128.00 | 5,460,999,489.00 | 15,869.00 | 100,546.00 | 9.40 | 451,270.00 | 7,070,634,612.00 | 15,668.30 | 148,822.00 | 8.53 | 375,419.00 | 6,277,227,410.00 | 0.89 | 16,720.59 | 148,822.00 | 9.28 |
20161114_Spenn_007_011 (211GB) | 20161114_Spenn_007_011 | 20161114_Spenn_007_011 | 92,994.00 | 1,334,258,832.00 | 14,348.00 | 107,121.00 | 8.59 | 66,439.00 | 1,035,193,238.00 | 15,581.00 | 90,489.00 | 9.39 | 93,032.00 | 1,399,668,682.00 | 15,045.02 | 114,980.00 | 8.34 | 72,447.00 | 1,187,443,861.00 | 0.85 | 16,390.52 | 88,575.00 | 9.28 |
20161116_Spenn_009_012 (799GB) | 20161116_Spenn_009_012 | 20161116_Spenn_009_012 | 523,760.00 | 5,360,546,441.00 | 10,238.00 | 162,037.00 | 9.00 | 430,481.00 | 4,558,323,604.00 | 10,589.00 | 67,428.00 | 9.54 | 523,757.00 | 5,650,882,208.00 | 10,789.13 | 141,897.00 | 8.98 | 459,425.00 | 5,129,078,435.00 | 0.91 | 11,164.13 | 89,621.00 | 9.47 |
20161116_Spenn_009_013 (250GB) | 20161116_Spenn_009_013 | 20161116_Spenn_009_013 | 166,466.00 | 1,717,528,003.00 | 10,317.00 | 114,435.00 | 8.98 | 134,116.00 | 1,441,345,290.00 | 10,747.00 | 56,948.00 | 9.57 | 166,552.00 | 1,803,799,080.00 | 10,830.25 | 65,727.00 | 8.92 | 141,882.00 | 1,599,743,855.00 | 0.89 | 11,275.17 | 59,889.00 | 9.50 |
20161118_Spenn_008_014 (174GB) | 20161118_Spenn_008_014 | 20161118_Spenn_008_014 | 122,505.00 | 1,146,492,883.00 | 9,358.00 | 146,319.00 | 8.96 | 99,017.00 | 961,490,600.00 | 9,710.00 | 58,788.00 | 9.59 | 123,625.00 | 1,200,962,979.00 | 9,714.56 | 175,642.00 | 8.81 | 105,539.00 | 1,080,066,667.00 | 0.90 | 10,233.82 | 61,659.00 | 9.48 |
20161118_Spenn_008_015 (296GB) | 20161118_Spenn_008_015 | 20161118_Spenn_008_015 | 186,513.00 | 1,815,953,333.00 | 9,736.00 | 181,283.00 | 8.84 | 148,452.00 | 1,495,777,948.00 | 10,075.00 | 62,177.00 | 9.50 | 186,910.00 | 1,902,441,366.00 | 10,178.38 | 131,748.00 | 8.80 | 159,309.00 | 1,696,083,933.00 | 0.89 | 10,646.50 | 66,511.00 | 9.41 |
20161121_Spenn_011_016 (727GB) | 20161121_Spenn_011_016 | 20161121_Spenn_011_016 | 328,053.00 | 4,215,219,836.00 | 12,849.00 | 161,459.00 | 8.84 | 260,702.00 | 3,485,323,522.00 | 13,368.00 | 81,602.00 | 9.50 | 328,267.00 | 4,414,265,051.00 | 13,447.18 | 137,344.00 | 8.79 | 280,747.00 | 3,952,418,629.00 | 0.90 | 14,078.22 | 120,499.00 | 9.41 |
20161121_Spenn_011_017 (423GB) | 20161121_Spenn_011_017 | 20161121_Spenn_011_017 | 203,146.00 | 2,594,558,262.00 | 12,771.00 | 153,016.00 | 8.79 | 155,876.00 | 2,105,331,803.00 | 13,506.00 | 88,254.00 | 9.50 | 203,279.00 | 2,720,576,015.00 | 13,383.46 | 238,936.00 | 8.66 | 167,707.00 | 2,386,049,312.00 | 0.88 | 14,227.49 | 105,080.00 | 9.40 |
20161123_Spenn_012_018 (650GB) | 20161123_Spenn_012_018 | 20161123_Spenn_012_018 | 327,709.00 | 3,870,110,250.00 | 11,809.00 | 180,596.00 | 8.76 | 254,308.00 | 3,133,636,771.00 | 12,322.00 | 85,535.00 | 9.49 | 328,350.00 | 4,036,113,614.00 | 12,292.11 | 129,774.00 | 8.68 | 273,662.00 | 3,544,343,780.00 | 0.88 | 12,951.54 | 90,413.00 | 9.39 |
20161123_Spenn_012_019 (896GB) | 20161123_Spenn_012_019 | 20161123_Spenn_012_019 | 499,116.00 | 5,886,334,951.00 | 11,793.00 | 167,972.00 | 8.87 | 392,448.00 | 4,878,338,636.00 | 12,430.00 | 118,685.00 | 9.51 | 499,824.00 | 6,171,272,387.00 | 12,346.89 | 145,910.00 | 8.73 | 419,542.00 | 5,488,400,148.00 | 0.89 | 13,081.88 | 88,850.00 | 9.41 |
20161123_Spenn_012_020 (646GB) | 20161123_Spenn_012_020 | 20161123_Spenn_012_020 | 370,723.00 | 4,223,196,504.00 | 11,391.00 | 181,030.00 | 8.92 | 290,213.00 | 3,500,334,970.00 | 12,061.00 | 90,173.00 | 9.54 | 371,609.00 | 4,443,108,401.00 | 11,956.41 | 108,644.00 | 8.79 | 316,526.00 | 4,017,146,779.00 | 0.90 | 12,691.36 | 96,971.00 | 9.44 |
20161125_Spenn_010_021 (564GB) | 20161125_Spenn_010_021 | 20161125_Spenn_010_021 | 416,857.00 | 3,459,880,516.00 | 8,299.00 | 150,499.00 | 8.88 | 335,613.00 | 2,913,698,492.00 | 8,681.00 | 56,044.00 | 9.46 | 417,487.00 | 3,627,019,345.00 | 8,687.74 | 169,514.00 | 8.72 | 356,707.00 | 3,266,344,223.00 | 0.90 | 9,156.94 | 169,514.00 | 9.34 |
20161130_Spenn_014_022 (277GB) | 20161130_Spenn_014_022 | 20161130_Spenn_014_022 | 144,680.00 | 1,763,487,955.00 | 12,188.00 | 188,526.00 | 8.95 | 115,211.00 | 1,490,693,758.00 | 12,938.00 | 77,113.00 | 9.52 | 144,841.00 | 1,840,563,228.00 | 12,707.47 | 108,006.00 | 8.75 | 122,432.00 | 1,661,746,134.00 | 0.90 | 13,572.81 | 80,884.00 | 9.44 |
20161130_Spenn_014_023 (559GB) | 20161130_Spenn_014_023 | 20161130_Spenn_014_023 | 249,427.00 | 3,061,683,900.00 | 12,274.00 | 169,609.00 | 8.64 | 186,877.00 | 2,447,344,412.00 | 13,096.00 | 93,030.00 | 9.39 | 249,648.00 | 3,180,153,904.00 | 12,738.55 | 107,542.00 | 8.43 | 203,528.00 | 2,811,421,534.00 | 0.88 | 13,813.44 | 98,174.00 | 9.27 |
20161130_Spenn_014_024 (851GB) | 20161130_Spenn_014_024 | 20161130_Spenn_014_024 | 395,151.00 | 5,042,395,024.00 | 12,760.00 | 230,409.00 | 8.61 | 294,534.00 | 3,946,433,116.00 | 13,398.00 | 78,966.00 | 9.41 | 396,516.00 | 5,297,048,958.00 | 13,358.98 | 358,713.00 | 8.54 | 326,870.00 | 4,604,556,443.00 | 0.87 | 14,086.81 | 124,229.00 | 9.26 |
20161202_Spenn_016_025 (784GB) | 20161202_Spenn_016_025 | 20161202_Spenn_016_025 | 371,137.00 | 4,578,018,827.00 | 12,335.00 | 192,749.00 | 8.63 | 280,153.00 | 3,604,968,054.00 | 12,867.00 | 109,370.00 | 9.41 | 372,149.00 | 4,791,498,491.00 | 12,875.22 | 149,406.00 | 8.50 | 303,673.00 | 4,150,146,602.00 | 0.87 | 13,666.50 | 149,406.00 | 9.26 |
20161202_Spenn_016_026 (827GB) | 20161202_Spenn_016_026 | 20161202_Spenn_016_026 | 431,745.00 | 5,333,852,075.00 | 12,354.00 | 202,965.00 | 8.68 | 326,658.00 | 4,214,255,431.00 | 12,901.00 | 153,099.00 | 9.43 | 432,622.00 | 5,622,615,652.00 | 12,996.60 | 672,474.00 | 8.74 | 365,112.00 | 4,939,809,559.00 | 0.88 | 13,529.57 | 99,452.00 | 9.35 |
20161202_Spenn_016_027 (949GB) | 20161202_Spenn_016_027 | 20161202_Spenn_016_027 | 484,175.00 | 6,103,006,087.00 | 12,604.00 | 305,986.00 | 8.68 | 371,827.00 | 4,859,413,464.00 | 13,069.00 | 79,985.00 | 9.42 | 485,163.00 | 6,430,996,802.00 | 13,255.33 | 374,023.00 | 8.72 | 410,406.00 | 5,645,415,708.00 | 0.88 | 13,755.69 | 111,014.00 | 9.31 |
20161204_Spenn_015_028 (512GB) | 20161204_Spenn_015_028 | 20161204_Spenn_015_028 | 251,396.00 | 2,705,390,485.00 | 10,761.00 | 140,518.00 | 8.58 | 182,745.00 | 2,111,380,840.00 | 11,553.00 | 83,721.00 | 9.42 | 253,480.00 | 2,798,547,416.00 | 11,040.51 | 117,952.00 | 8.24 | 197,682.00 | 2,416,371,861.00 | 0.86 | 12,223.53 | 83,321.00 | 9.29 |
20161204_Spenn_015_029 (600GB) | 20161204_Spenn_015_029 | 20161204_Spenn_015_029 | 317,257.00 | 3,566,412,110.00 | 11,241.00 | 253,497.00 | 8.76 | 244,735.00 | 2,884,284,143.00 | 11,785.00 | 97,690.00 | 9.51 | 320,491.00 | 3,742,222,498.00 | 11,676.53 | 766,390.00 | 8.58 | 264,535.00 | 3,283,863,360.00 | 0.88 | 12,413.72 | 127,189.00 | 9.38 |
20161206_Spenn_017_030 (1.2TB) | 20161206_Spenn_017_030 | 20161206_Spenn_017_030 | 1,133,214.00 | 7,324,445,582.00 | 6,463.00 | 163,606.00 | 8.89 | 908,610.00 | 6,019,467,101.00 | 6,625.00 | 94,944.00 | 9.55 | 1,133,449.00 | 7,694,792,575.00 | 6,788.83 | 144,140.00 | 8.89 | 970,352.00 | 6,779,404,141.00 | 0.88 | 6,986.54 | 118,872.00 | 9.46 |
20161206_Spenn_017_031 (1.1TB) | 20161206_Spenn_017_031 | 20161206_Spenn_017_031 | 1,009,641.00 | 7,161,552,200.00 | 7,093.00 | 228,704.00 | 8.87 | 798,551.00 | 5,802,073,420.00 | 7,266.00 | 108,965.00 | 9.59 | 1,010,016.00 | 7,572,683,619.00 | 7,497.59 | 573,773.00 | 9.00 | 869,908.00 | 6,682,822,091.00 | 0.88 | 7,682.22 | 185,132.00 | 9.53 |
- MiSeq data
- NextSeq data used for independent error correction
- NextSeq data for accession LA2963
- assembly data
Assembly | N50 | L50 | Total size | Largest contig | Total contigs | Illumina mapping rate % | Qualimap Discrepancy rate | % complete BUSCO |
Canu (929MB) | 1.55 | 169 | 961.83 | 10.01 | 2010 | 98.95 | 0.82 | 96.46 |
SMARTdenovo (923MB) | 1.06 | 270 | 955.31 | 5.84 | 1901 | 98.99 | 0.91 | 96.11 |
Miniasm (945MB) | 1.75 | 156 | 977.78 | 9.49 | 2704 | 98.24 | 2.48 | 85.69 |
CanuSMARTdenovo (885MB) | 2.52 | 106 | 915.60 | 12.72 | 899 | 98.98 | 0.85 | 96.46 |
All sequence length in Mbp
All assemblies are 5x pilon polished
- gene model data
augustus04_filtered.gff | GFF file |
augustus04_filtered.gff | Protein sequences |
augustus04_filtered.gff | Nucleotide sequences |
Acknowledgement
We want to acknowledge partial funding through the Federal Ministry of Education and Research (0315961, 031A053, and 031A536C), the Ministry of Innovation, Science, and Research within the framework of the NRW Strategieprojekt BioSC (313/323-400-002 13), the Deutsche Forschungsgemeinschaft (Grants US98/7-1 and FE552/29-1) within ERACAPS Regulatome, and support for large equipment from Deutsche Forschungsgemeinschaft (Grossgeräte NextSeq LC-MS) and France Génomique (ANR-10-INBS-09). D.Z. was supported by the Horizon-2020 Grant G2P-SOL (677379). S.K. was supported in part by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health. This work utilized the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov).