Project name: Acyrthosiphon pisum isolate:LSR1

Description: This study aimed at comparing the global X chromosome and autosomes chromatin accessibility between Acyrthosiphon pisum males and parthenogenetic females.Aphid individuals from the clone LSR1 (the reference clone that was used for genome sequencing (34)) were reared on broad bean Vicia faba at low density (less than five individuals per plant) to prevent the production of winged morphs for at least two generations. Parthenogenesis was maintained under a 16 h photoperiod and a temperature of 18°C. At the third generation, 20 asexual females were then directly frozen into liquid nitrogen for FAIRE extraction. The production of male individuals was initiated by transferring larvae from a 16 h to a 12 h photoperiod at the same temperature of 18°C (31). Two generations later, sexual females and males were observed. A total of 100 adult males were then directly frozen into liquid nitrogen for FAIRE extraction.Tissues were first grinded using a Biospec Bio-pulverizer and then fixed by the addition of 3% of Thermo Scientific Pierce formaldehyde during 8 minutes. The fixation was then stopped by the addition of glycine at 125mM. Subsequently to the pellet rinsing and resuspension, the tissues were grinded with a Tissue Lyser, using Qiagen metallic beads, during 5 cycles of 5 minutes, each being interrupted during 2 minutes. The sonication steps have been performed using a Bioruptor Plus during 12 cycles of 30 seconds, each being interrupted during 30 seconds. Phenol chloroform extraction steps have been performed using Sigma phenol chloroform. Subsequently to its extraction, the FAIRE DNA is purified the using ZYMO ChIP DNA Clean & Concentrator. Finally, FAIRE and Control DNA were quantified using a Quantus with the Quantifluor dsDNA kit.FAIRE and Control DNA were sequenced using the Illumina Hiseq 2000 instrument and ChIP TrueSeq kit. Three FAIRE Samples for each sex were sequenced, while only a pool of the three samples from same sex individuals was sequenced for control DNA. The 8 different samples (6 FAIRE and 2 Control Samples) were 100pb paired-end sequenced on a single lane.

Data type: epigenomics

Sample scope: Monoisolate

Relevance: Agricultural

Last updated: 2016-10-13