Table 1.
Metaseiulus occidentalis Genome Assembly and Gene Set Statistics Compared with Eight Other Arachnids
| Acari: Parasitiformes | Acari: Acariformes | Araneae | Scorpiones | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Species | Metaseiulus occidentalis | Varroa destructor | Ixodes scapularis | Dermatophagoides farinae | Sarcoptes scabiei | Tetranychus urticae | Stegodyphus mimosarum | Acanthoscurria geniculata | Mesobuthus martensii |
| Organism | Western orchard predatory mite | Honey bee parasitic mite | Black-legged deer tick | American house dust mite | Itch mite (scabies) | Two-spotted spider mite | African social velvet spider | Brazilian white-knee tarantula | Chinese scorpion |
| Assembly | GCA_000255335.1 | GCA_000181155.1 | GCA_000208615.1 | GCA_000767015.1 | GCA_000828355.1 | GCA_000239435.1 | GCA_000611955.2 | GCA_000661875.1 | GCA_000484575.1 |
| Assembly method | Celera v.6.1 | Celera v.5.2 | Celera v.4.0 | AllPaths v.39075 | Minia v.1.6088 | Arachne 20071016 | SOAPdenovo v.2 | SOAPdenovo v.2 | Velvet v.1.1.04 |
| Velvet v.1.1.03 | SSPACE | ||||||||
| SOAPdenovo v.1.05 | Standard v.3.0 | ||||||||
| Coverage (×) | 17.7 | 5 | 6 | 436 | 174 | 8a | 70 | 70 | 200 |
| Assembly length (Mb) | 151.7 | 294.1 | 1,765.4 | 53.5 | 56.3 | 90.8 | 2,738.7 | 7,178.4 | 925.5 |
| 1,128.5b | |||||||||
| No. of Contigs | 3,993 | 184,190 | 570,637 | 11,600 | 19,811 | 2,035 | 174,164 | 12,478,692 | 92,408 |
| 18,600c | |||||||||
| Contig N50 (bp) | 200,706 | 2,262 | 2,942 | 8,538 | 11,197 | 212,780 | 40,146 | 541 | 45,228 |
| 11.6 kbc | 17,272d | 277d | 43,135b | ||||||
| No. of scaffolds | 2,211 | na | 369,492 | 515 | na | 640 | 68,653 | na | na |
| Scaffold N50 (bp) | 896,831 | na | 76,228 | 186,342 | na | 2,993,488 | 480,636 | 47,837d | 223,560b |
| No. of protein-coding genes | 18,338e | 11,432g | 20,486h | 16,376i | 10,473 | 18,414a | 27,135 | 73,821k | 32,016b |
| 11,430f | 10,644c | 18,224j | 27,235d | ||||||
| % CEGsl | 98.0/96.8 | 67.7/32.3 | 79.8/41.9 | 97.6/96.4 | 98.0/93.5 | 98.0/95.2 | 61.7/24.2 | 32.7/14.9 | 57.3/24.2 |
| % BUSCOsm(assembly) | 82.3 [6.4], 8.3, 9.9 | 15.2 [0.5], 15.4, 69.5 | 68.9 [2.4], 21.0, 10.1 | 63.8 [3.5], 7.6, 28.6 | 62.0 [3.0], 8.4, 29.6 | 68.8 [5.8], 9.9, 21.3 | 53.7 [4.0], 27.4, 18.9 | 13.7 [1.9], 10.6, 75.7 | 34.4 [4.0], 23.0, 42.7 |
| % BUSCOsm(gene set) | 82.8 [12.0], 10.6, 6.5 | na | 69.4 [6.7], 23.4, 7.2 | na | 54.0 [4.7], 11.4, 34.6 | 69.3 [11.4], 9.6, 21.0 | 64.6 [10.5], 17.3, 18.1 | na | 23.1 [6.7], 16.4, 60.5 |
Note.—Unless otherwise indicated, values were retrieved from the NCBI.
From Grbić et al. (2011).
From Cao et al. (2013).
From Rider et al. (2015).
From Sanggaard et al. (2014).
NCBI Gnomon gene set.
NCBI RefSeq gene set.
Identified open-reading frames with significant sequence similarity to database sequences from Cornman et al. (2010).
IscaW1.4 gene set from VectorBase (www.vectorbase.org).
From Chan et al. (2015).
From EnsemblGenomes (http://metazoa.ensembl.org).
From Sanggaard et al. (2014), transcripts of more than 17 amino acids.
% of 248 CEGMA genes Found/Complete, in the assembly.
% of 2,675 arthropod BUSCOs Complete [Duplicated], Fragmented, Missing, in the assembly or in the gene set.