The Chondrus crispus genome – Supplementary material 1 Genome sequencing, assembly and annotation .................................................................................... 4 1.1 Sequencing .................................................................................................................................... 4 1.2 Genome assembly .......................................................................................................................... 4 1.3 Annotation pipeline ....................................................................................................................... 4 1.4 Expert annotation .......................................................................................................................... 6 1.5 Intron conservation profiles in orthologous proteins ..................................................................... 7 1.6 Contamination verification .......................................................................................................... 11 2 Genome and gene structure ................................................................................................................ 12 2.1 Plastid genome ............................................................................................................................ 12 2.2 Mitochondrial genome ................................................................................................................ 12 2.3 Organellar sequences in the nuclear genome .............................................................................. 12 2.4 Codon usage ................................................................................................................................ 13 2.5 Transposable elements ................................................................................................................ 14 2.6 Selenoproteins ............................................................................................................................. 17 2.7 Large scale duplication analysis .................................................................................................. 18 2.8 Transcription factors and transcriptional regulators .................................................................... 20 3 Evolutionary studies ........................................................................................................................... 21 3.1 Comparison with other red algae. ................................................................................................ 21 3.2 The phylome ................................................................................................................................ 21 3.3 Phylogeny-based orthology prediction ........................................................................................ 22 3.4 Species tree .................................................................................................................................. 22 3.5 Lineage specific duplications ...................................................................................................... 23 3.6 Comparative genome analysis ..................................................................................................... 24 3.7 Horizontal transfer ....................................................................................................................... 27 4 Replication, transcription and translation ........................................................................................... 27 4.1 The exosome complex ................................................................................................................. 27 4.2 Spliceosome................................................................................................................................. 28 4.3 mRNA maturation ....................................................................................................................... 28 4.4 DNA Replication ......................................................................................................................... 30 4.5 DNA Repair and recombination .................................................................................................. 31 4.6 Meiosis ........................................................................................................................................ 31 4.7 Chromatin modifying genes ........................................................................................................ 32 4.8 RecQ helicase .............................................................................................................................. 34 1 4.9 Initiation factors .......................................................................................................................... 35 4.10 Ribosomal proteins .................................................................................................................... 36 5 Cell structure and regulation .............................................................................................................. 38 5.1 Cytoskeleton ................................................................................................................................ 38 5.2 Vesicle trafficking ....................................................................................................................... 41 5.3 Kinases ........................................................................................................................................ 46 5.4 The GTPase regulation ................................................................................................................ 47 6 Photosynthesis and respiration ........................................................................................................... 55 6.1 Light-harvesting complexes ........................................................................................................ 55 6.2 Pigment biosynthesis ................................................................................................................... 56 6.3 Photoreceptors and circadian clock players ................................................................................ 56 6.4 Carbon uptake.............................................................................................................................. 57 6.5 Oxidative phosphorylation .......................................................................................................... 58 7 Metabolism ......................................................................................................................................... 63 7.1 Amino acid metabolism ............................................................................................................... 63 7.2 Nitrogen uptake ........................................................................................................................... 65 7.3 Urea metabolism and urea cycle.................................................................................................. 65 7.4 Gamma-aminobutyric acid .......................................................................................................... 66 7.5 Proline metabolism ...................................................................................................................... 66 7.6 Fatty acid metabolism ................................................................................................................. 67 7.7 Carbon storage and cell wall metabolism .................................................................................... 75 7.8 Polysaccharide sulphate active enzymes ..................................................................................... 80 7.9 Sulphotransferases ....................................................................................................................... 80 7.10 Sulphurylases............................................................................................................................. 84 7.11 Sulphatases ................................................................................................................................ 85 7.12 Starch ......................................................................................................................................... 85 7.13 Mannitol metabolism ................................................................................................................. 89 7.14 Lignin biosynthesis .................................................................................................................... 90 7.15 General secondary metabolism.................................................................................................. 91 7.16 Glutathione S-transferases ......................................................................................................... 96 8 Defence-related and stress genes ...................................................................................................... 100 8.1 Candidate pathogen receptors or resistance genes. ................................................................... 100 8.2 Candidate defence effectors ...................................................................................................... 102 8.3 Halogen metabolism .................................................................................................................. 103 2 8.4