Sequencing and Analysis of Recombinant Inbred Lines of the cross Lactuca sativa and Lactuca serriola
Genomic DNA was isolated from leaves of Lactuca sativa, Lactuca serriola and the RILs using a modified CTAB extraction method [Rogers et al.]. DNA samples were fragmented to lengths of ∼300 bp by sonication using a UCD-200 Bioruptor as per the manufacturer’s instructions (Diagenode, Inc., Denville, NJ, USA). Genomic paired-end libraries were then prepared using standard procedures and NEB reagents for end-repair, A-tailing, and adapter ligation. All libraries were PCR amplified using the high-fidelity Phusion polymerase. The RIL libraries were indexed using sequencing adapters with 6-bp in-line barcodes, and pooled into three subsets (A, B, and C). Aliquots of the libraries were normalized using a Duplex-Specific Nuclease protocol [Matvienko et al.]. See bar-code conversion table below.    References:    - Rogers SO, Bendich AJ (1988) Extraction of DNA from plant tissues. In: Plant Molecular Biology Manual, Gelvin SB and Schilperoort RA (eds), Kluwer Academic Publishers, Dordrecht, The Netherlands, 1–10.    - Matvienko M, Kozik A, Froenicke L, Lavelle D, Martineau B, Perroud B, Michelmore R. Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride. PLoS One. 2013;8(2)    *** Bar-code conversion:    *** Pool A:  TGTAC R020 Pool_A;  AACCC R031 Pool_A;  CAACT R032 Pool_A;  GAATC R033 Pool_A;  TAAGC R040 Pool_A;  AAGCG R044 Pool_A;  CATAG R047 Pool_A;  GACAC R050 Pool_A;  TACAG R062 Pool_A;  ACACG R063 Pool_A;  CCATC R067 Pool_A;  GAGTA R068 Pool_A;  TAGCT R069 Pool_A;  ACCTA R071 Pool_A;  CCTCT R072 Pool_A;  GATGT R074 Pool_A;  TCAAG R078 Pool_A;  ACGAT R083 Pool_A;  CGCTA R084 Pool_A;  GATTG R085 Pool_A;  TCCAC R096 Pool_A;  ACTAC R097 Pool_A;  CGTAT R101 Pool_A;  GCAGA R111 Pool_A;  TCGAA R112 Pool_A;  AGCCA R116 Pool_A;  CTAGT R118 Pool_A;  GCCAT R120 Pool_A;  TCTGG R121 Pool_A;  AGCTC R123 Pool_A;  CTCTG R128 Pool_A;  GCGTT R235 Pool_A;  GTCGC R237 Pool_A;  ATGCA R257 Pool_A;  GTGAG R320 Pool_A;    *** Pool B:  AACCC R002 Pool_B;  CAACT R007 Pool_B;  GAATC R019 Pool_B;  TAAGC R022 Pool_B;  AAGCG R023 Pool_B;  CATAG R025 Pool_B;  GACAC R026 Pool_B;  TACAG R029 Pool_B;  ACACG R070 Pool_B;  CCATC R081 Pool_B;  GAGTA R089 Pool_B;  TAGCT R090 Pool_B;  ACCTA R238 Pool_B;  CCTCT R239 Pool_B;  GATGT R240 Pool_B;  TCAAG R242 Pool_B;  AGGTT R278 Pool_B;  CTGCT R280 Pool_B;  GGACT R283 Pool_B;  TGCGT R291 Pool_B;  AGTCG R299 Pool_B;  GGTAA R300 Pool_B;  TGGAG R301 Pool_B;  ATCGG R302 Pool_B;  GTCGC R306 Pool_B;  TGTAC R307 Pool_B;  ATGCA R312 Pool_B;  GTGAG R315 Pool_B;  TTAGG R318 Pool_B;  ATTGC R321 Pool_B;  GTTAC R325 Pool_B;  TTTCC R326 Pool_B;    *** Pool C:  ACGAT R244 Pool_C;  CGCTA R247 Pool_C;  GATTG R249 Pool_C;  TCCAC R250 Pool_C;  ACTAC R252 Pool_C;  CGTAT R253 Pool_C;  GCAGA R255 Pool_C;  TCGAA R256 Pool_C;  AGCCA R258 Pool_C;  CTAGT R260 Pool_C;  GCCAT R263 Pool_C;  TCTGG R265 Pool_C;  AGCTC R266 Pool_C;  CTCTG R267 Pool_C;  GCGTT R268 Pool_C;  TGATG R270 Pool_C;  AGGTT R327 Pool_C;  CTGCT R329 Pool_C;  GGACT R330 Pool_C;  TGCGT R336 Pool_C;  AGTCG R339 Pool_C;  GGTAA R343 Pool_C;  TGGAG R344 Pool_C;  ATCGG R345 Pool_C;  GTCGC R346 Pool_C;  TGTAC R348 Pool_C;  ATGCA R350 Pool_C;  GTGAG R358 Pool_C;  TTAGG R362 Pool_C;  ATTGC R364 Pool_C;  GTTAC R369 Pool_C;  TTTCC R370 Pool_C;    ***