Pea Aphid (Acyrthosiphon pisum) genome was sequenced at 15X coverage using Illumina HiSeq technology. An average of 42.5 million 100bp reads with mean insert size of 250bp were generated. All the Scaffold were used as input to MIcroSAtellite identification tool (MISA) to identify and find the location of perfect and compound microsatellites.


Scientific nameCommon nameOrderChr. no.Genome Size (MB)GC%
Acyrthosiphon pisumPea AphidHomoptera1-23925464MB29.6%


Table 1. Description of Pea Aphid genome
TypeNumberPercentage
Simple30459589.53
Compound3419610.05
Complex14420.42
Total340233100.00

**Note that in Table-1, we reported 340233 total SSRs because we counted only the compound SSR as one time although this may have more than one Simple repeats.



Table 2. Distribution of Simple microsatellite types in pea aphid genome
Motif TypeNumberPercentage of Simple(%)Percentage of Total (%)
Mono22361173.4165.72
Di4177013.7112.28
Tri3638911.9510.70
Tetra21450.700.63
Penta6000.200.18
Hexa800.030.02




Table 3. Length distribution of Simple microsatellite types in pea aphid genome
LengthNumberPercentage of Simple(%)
>=109638531.64
11-1515450050.72
16-203146610.33
21-25117413.85
26-3055081.81
31-3515930.52
36-4014260.47
41-456510.21
46-503810.13
>=509440.31




References:

1. Gouin et al. (2015) Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads. Heredity
2. Jaquiery et al. (2012) Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex.Molecular Ecology
3. International Genome Consortium (2010) Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biology 4. Weng et al. (2007) Cross-species transferability of microsatellite markers from six aphid (Hemiptera: Aphididae) species and their use for evaluating biotypic diversity in two cereal aphids. Insect Molecular Biology
5. Caillaud et al.(2004) Microsatellite DNA markers for the pea aphid Acyrthosiphon pisum. Molecular Ecology Notes
6. Kurokawa et al.(2004) Isolation of six microsatellite markers from the pea aphid, Acyrthosiphon pisum (Homoptera, Aphididae). Molecular Ecology Notes