Status
Assembly v3 (25 September 2011) is a draft assembly of 454 and Solexa gDNA reads. A total of 414 scaffolds and 34.6 Mbp were assembled using Velvet and then Newbler.
This genome sequence and gene prediction of the Cladonia grayi mycobiont were not determined by the JGI, but were acquired from Olaf Mueller at Duke U. on September 25 2011. This copy of the genome does not include the mitochondrial chromosomes or genes. The JGI Annotation Pipeline was used to add additional functional annotation to Duke's scaffolds and gene models.
Summary statistics for the Cladonia grayi Cgr/DA2myc/ss
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 34.62 |
| Sequencing read coverage depth | 15x |
| # of contigs | 519 |
| # of scaffolds | 414 |
| # of scaffolds >= 2Kbp | 414 |
| Scaffold N50 | 43 |
| Scaffold L50 (Mbp) | 0.24 |
| # of gaps | 105 |
| % of scaffold length in gaps | 0.2% |
| Three largest Scaffolds (Mbp) | 0.96, 0.83, 0.76 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | 454_ESTs | 740680 | 564099 | 76.2% |
| Other | Newbler_contigs | 17471 | 12252 | 70.1% |
| Other | Velvet_and_Trinity_contigs | 17986 | 17878 | 99.4% |
| Gene Models | Maker | |
| length (bp) of: | average | median |
| gene | 1807 | 1525 |
| transcript | 1651 | 1385 |
| exon | 545 | 320 |
| intron | 79 | 58 |
| description: | ||
| protein length (aa) | 477 | 388 |
| exons per gene | 3.03 | 3 |
| # of gene models | 11389 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM Jr, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB
The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.
BMC Genomics. 2019 Jul 23;20(1):605. doi: 10.1186/s12864-019-5629-x
Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM Jr, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB
The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.
BMC Genomics. 2019 Jul 23;20(1):605. doi: 10.1186/s12864-019-5629-x
Funding
This project was not sequenced at the JGI.
