Introduction

This document review and summarize sequence capture and genomic analysis of Symphonia globulifera.

0.1 Modus operandi (to discuss):

We will proceed sequence capture and genomic analysis of Symphonia globulifera with following steps:

  • [x] Choose kit
  • [x] Select sequence to be captured
  • [x] Extract DNA
  • [ ] Prepare libraries
  • [ ] Raw data analysis
    • [ ] Genome by Sequencing (GbS)
    • [ ] Reads mapping
    • [ ] SNP call
    • [ ] SNP filtering
  • [ ] Genetic data analysis
    • [ ] Genetic structure of populations
    • [ ] Genomic structure of polymorphisms
    • [ ] Ecological genomic (genotype-environment association)
    • [ ] Assocaition genomic (genotype-phenotype association)

Figure 0.1: Different types in which to choose sequences to capture. CDS stand for Coding DNA sequence and UTR for UnTranscribed Region.

0.2 Sequence selection

Selection of target sequences is based on following scheme 0.2:

Schemes of selection of target sequences.

Figure 0.2: Schemes of selection of target sequences.

0.3 Lexicon

  • nuclear gene
  • isoform
  • scaffold
  • transcript
  • gene sensu Trinity