The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions
- Heinrich Heine University, Germany
- Rutgers University, United States
- Arizona State University, United States
Figures
Figure 1
Geographic origin and habitat description of the analyzed Cyanidiales strains.
Available reference genomes are marked with an asterisk (*), whereas ‘na’ indicates missing information.
Figure 2
Species tree of the 13 analyzed extremophilic Cyanidiales genomes using mesophilic red (Porphyra umbilicalis, Porphyridium purpureum) and green algae (Ostreococcus tauri, Chlamydomonas reinhardtii) as outgroups.
IQTREE was used to infer a single maximum-likelihood phylogeny based on orthogroups containing single-copy representative proteins from at least 12 of the 17 taxa (13 Cyanidiales + 4 Others). Each …
Figure 3
Differential gene expression of G. sulphuraria 074W.
(A) and C. merolae 10D (B), here measured as log fold change (logFC) vs transcription rate (logCPM). Differentially expressed genes are colored red (quasi-likelihood (QL) F-test, Benjamini-Hochberg, …
Figure 4
Comparative analysis of the 96 OGs potentially derived from HGT.
(A) OG count vs. the number of Cyanidiales species contained in an OG (=OG size). Only genes from the sequenced genomes were considered (13 species). A total of 60 OGs are exclusive to the Galdieria …
Figure 5 with 96 supplements
The analysis of OGs containing HGT candidates revealed different patterns of HGT acquisition.
Some OGs contain genes that are shared by all Cyanidiales, whereas others are unique to the Galdieria or Cyanidioschyzon lineage. In some cases, HGT appears to have replaced the eukaryotic genes in …
Figure 5—figure supplement 1
Sequence tree of orthogroup OG0001476.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 2
Sequence tree of orthogroup OG0001486.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 3
Sequence tree of orthogroup OG0001509.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 4
Sequence tree of orthogroup OG0001513.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 5
Sequence tree of orthogroup OG0001542.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 6
Sequence tree of orthogroup OG0001613.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 7
Sequence tree of orthogroup OG0001658.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 8
Sequence tree of orthogroup OG0001760.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 9
Sequence tree of orthogroup OG0001807.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 10
Sequence tree of orthogroup OG0001810.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 11
Sequence tree of orthogroup OG0001929.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 12
Sequence tree of orthogroup OG0001938.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 13
Sequence tree of orthogroup OG0001955.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 14
Sequence tree of orthogroup OG0001976.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 15
Sequence tree of orthogroup OG0001994.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 16
Sequence tree of orthogroup OG0002036.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 17
Sequence tree of orthogroup OG0002051.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 18
Sequence tree of orthogroup OG0002191.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 19
Sequence tree of orthogroup OG0002305.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 20
Sequence tree of orthogroup OG0002337.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 21
Sequence tree of orthogroup OG0002431.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 22
Sequence tree of orthogroup OG0002483.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 23
Sequence tree of orthogroup OG0002574.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 24
Sequence tree of orthogroup OG0002578.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 25
Sequence tree of orthogroup OG0002609.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 26
Sequence tree of orthogroup OG0002676.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 27
Sequence tree of orthogroup OG0002727.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 28
Sequence tree of orthogroup OG0002785.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 29
Sequence tree of orthogroup OG0002871.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 30
Sequence tree of orthogroup OG0002896.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 31
Sequence tree of orthogroup OG0002999.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 32
Sequence tree of orthogroup OG0003085.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 33
Sequence tree of orthogroup OG0003250.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 34
Sequence tree of orthogroup OG0003367.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 35
Sequence tree of orthogroup OG0003441.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 36
Sequence tree of orthogroup OG0003539.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 37
Sequence tree of orthogroup OG0003777.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 38
Sequence tree of orthogroup OG0003782.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 39
Sequence tree of orthogroup OG0003834.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 40
Sequence tree of orthogroup OG0003846.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 41
Sequence tree of orthogroup OG0003856.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 42
Sequence tree of orthogroup OG0003901.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 43
Sequence tree of orthogroup OG0003905.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 44
Sequence tree of orthogroup OG0003907.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 45
Sequence tree of orthogroup OG0003929.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 46
Sequence tree of orthogroup OG0003954.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 47
Sequence tree of orthogroup OG0004030.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 48
Sequence tree of orthogroup OG0004102.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 49
Sequence tree of orthogroup OG0004142.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 50
Sequence tree of orthogroup OG0004203.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 51
Sequence tree of orthogroup OG0004258.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 52
Sequence tree of orthogroup OG0004339.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 53
Sequence tree of orthogroup OG0004392.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 54
Sequence tree of orthogroup OG0004405.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 55
Sequence tree of orthogroup OG0004486.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 56
Sequence tree of orthogroup OG0004658.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 57
Sequence tree of orthogroup OG0005083.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 58
Sequence tree of orthogroup OG0005087.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 59
Sequence tree of orthogroup OG0005153.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 60
Sequence tree of orthogroup OG0005224.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 61
Sequence tree of orthogroup OG0005235.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 62
Sequence tree of orthogroup OG0005280.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 63
Sequence tree of orthogroup OG0005479.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 64
Sequence tree of orthogroup OG0005540.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 65
Sequence tree of orthogroup OG0005561.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 66
Sequence tree of orthogroup OG0005596.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 67
Sequence tree of orthogroup OG0005683.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 68
Sequence tree of orthogroup OG0005694.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 69
Sequence tree of orthogroup OG0005738.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 70
Sequence tree of orthogroup OG0005963.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 71
Sequence tree of orthogroup OG0005984.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 72
Sequence tree of orthogroup OG0006136.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 73
Sequence tree of orthogroup OG0006143.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 74
Sequence tree of orthogroup OG0006191.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 75
Sequence tree of orthogroup OG0006251.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 76
Sequence tree of orthogroup OG0006252.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 77
Sequence tree of orthogroup OG0006435.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 78
Sequence tree of orthogroup OG0006482.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 79
Sequence tree of orthogroup OG0006498.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 80
Sequence tree of orthogroup OG0006623.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 81
Sequence tree of orthogroup OG0006670.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 82
Sequence tree of orthogroup OG0007051.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 83
Sequence tree of orthogroup OG0007123.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 84
Sequence tree of orthogroup OG0007346.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 85
Sequence tree of orthogroup OG0007383.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 86
Sequence tree of orthogroup OG0007550.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 87
Sequence tree of orthogroup OG0007551.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 88
Sequence tree of orthogroup OG0007596.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 89
Sequence tree of orthogroup OG0008189.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 90
Sequence tree of orthogroup OG0008334.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 91
Sequence tree of orthogroup OG0008335.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 92
Sequence tree of orthogroup OG0008579.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 93
Sequence tree of orthogroup OG0008680.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 94
Sequence tree of orthogroup OG0008822.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 95
Sequence tree of orthogroup OG0008898.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 5—figure supplement 96
Sequence tree of orthogroup OG0008996.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited …
Figure 6
HGT vs. non-HGT orthogroup comparisons.
(A) Maximum PID of Cyanidiales genes in native (blue) and HGT (yellow) orthogroups when compared to non-eukaryotic sequences in each OG. The red lines denote the 70% PID threshold for assembly …
Figure 7
Cyanidiales live in hostile habitats, necessitating a broad range of adaptations to polyextremophily.
The majority of the 96 HGT-impacted OGs were annotated and putative functions identified (in the image, colored fields are from HGT, whereas gray fields are native functions). The largest number of …
Appendix 1—figure 1
Raw read length distribution of the sequenced Cyanidiales strains.
The strains were sequenced in 2016/2017 using PacBio’s RS2 sequencing technology and P6-C4 chemistry (the only exception being C. merolae Soos, which was sequenced as pilot study using P4-C2 …
Appendix 3—figure 1
%GC – Galdieria sulphuraria 074W: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 2
%GC – Galdieria sulphuraria MS1: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 3
%GC – Galdieria sulphuraria RT22: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 4
%GC – Galdieria sulphuraria SAG21: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 5
%GC – Galdieria sulphuraria Mount Shasta (MtSh): (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 6
Galdieria sulphuraria Azora: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 7
%GC – Galdieria sulphuraria Mount Shasta YNP5578.1: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 8
%GC – Galdieria sulphuraria 5572: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 9
%GC – Galdieria sulphuraria 002: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 10
%GC – Galdieria phlegrea Soos: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 11
%GC – Galdieria phlegrea DBV009: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 12
%GC – Cyanidioschyzon merolae Soos: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 3—figure 13
%GC – Cyanidioschyzon merolae 10D: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC …
Appendix 4—figure 1
Exon/Intron – Galdieria sulphuraria 074W: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 2
Exon/Intron – Galdieria sulphuraria MS1: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 3
Exon/Intron – Galdieria sulphuraria RT22: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 4
Exon/Intron – Galdieria sulphuraria SAG21: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 5
Exon/Intron – Galdieria sulphuraria MtSh: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 6
Exon/Intron – Galdieria sulphuraria Azora: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 7
Exon/Intron – Galdieria sulphuraria YNP5578.1: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 8
Exon/Intron – Galdieria sulphuraria 5572: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 9
Exon/Intron – Galdieria sulphuraria 002: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 10
Exon/Intron – Galdieria phlegrea Soos: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 11
Exon/Intron – Cyanidioschyzon merolae Soos: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 4—figure 12
Exon/Intron – Cyanidioschyzon merolae 074W: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal …
Appendix 5—figure 1
Best Blast Hit between each of the 13 Cyanidiales species and their most similar non-eukaryotic Ortholog in each OG-phylogeny.
Values are given as average percent protein identity between Cyanidiales and non-eukaryotic ortholog. White boxes represent missing Cyanidiales orthologs.
Tables
Table 1
Summary of the 13 analyzed Cyanidiales genomes.
The existing genomes of Galdieria sulphuraria 074W, Cyanidioschyzon merolae 10D, and Galdieria phlegrea are marked with ‘#'. The remaining 10 genomes are novel. Genome Size (Mb): size of the genome …
| Strain | Genome features | Gene and OG counts | HGTs | HGT vs native gene subsets | Annotations | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genome Size (Mb) | Contigs | Contig N50 (kb) | %GC Content | Genes | Orthogroups | HGT orthogroups | HGT genes | %GC Native | %GC HGT | (%) Multiexon Native | (%) Multiexon HGT | Exon/Gene Native | Exon/Gene HGT | EC | PFAM | KEGG | GO | |
| G. sulphuraria 074W# | 13.78 | 433 | 172.3 | 36.89 | 7174 | 5265 | 51 | 55 | 38.99 | 39.62* | 73.6 | 47.3* | 2.25 | 3.2* | 938 | 3073 | 3241 | 6572 |
| G. sulphuraria MS1 | 14.89 | 129 | 172.1 | 37.62 | 7441 | 5389 | 54 | 58 | 39.59 | 40.79* | 83.4 | 62.1* | 2.5 | 3.88* | 930 | 3077 | 3178 | 6564 |
| G. sulphuraria RT22 | 15.62 | 118 | 172.9 | 37.43 | 6982 | 5186 | 51 | 54 | 39.54 | 40.85* | 74.7 | 51.9* | 2.63 | 3.95* | 941 | 3118 | 3223 | 6504 |
| G. sulphuraria SAG21 | 14.31 | 135 | 158.2 | 37.92 | 5956 | 4732 | 44 | 47 | 40.04 | 41.47* | 84.8 | 83.0 | 4.02 | 5.03* | 931 | 3047 | 3143 | 6422 |
| G. sulphuraria MtSh | 14.95 | 101 | 186.6 | 40.04 | 6160 | 4746 | 46 | 47 | 41.33 | 42.48* | 79.7 | 63.8* | 3.15 | 4.32* | 939 | 3114 | 3244 | 6450 |
| G. sulphuraria Azora | 14.06 | 127 | 162.3 | 40.10 | 6305 | 4905 | 49 | 58 | 41.34 | 42.57* | 84.5 | 75.9* | 2.68 | 4.03* | 934 | 3072 | 3181 | 6474 |
| G. sulphuraria YNP5587.1 | 14.42 | 115 | 170.8 | 40.05 | 6118 | 4846 | 46 | 46 | 41.33 | 42.14* | 74.5 | 54.3* | 2.61 | 3.65* | 938 | 3084 | 3206 | 6516 |
| G. sulphuraria 5572 | 14.28 | 108 | 229.7 | 37.99 | 6472 | 5009 | 46 | 53 | 39.68 | 40.5* | 78.4 | 45.3* | 2.15 | 3.53* | 936 | 3108 | 3252 | 6540 |
| G. sulphuraria 002 | 14.11 | 107 | 189.3 | 39.16 | 5912 | 4701 | 46 | 52 | 40.76 | 41.35* | 97.1 | 50.0* | 2.37 | 3.73* | 927 | 3060 | 3184 | 6505 |
| G. phlegrea DBV009# | 11.41 | 9311 | 2.0 | 37.86 | 7836 | 5562 | 54 | 62 | 39.97 | 40.58* | na | na | na | na | 935 | 3018 | 3125 | 6512 |
| G. phlegrea Soos | 14.87 | 108 | 201.1 | 37.52 | 6125 | 4624 | 44 | 47 | 39.57 | 40.73* | 77.5 | 43.2* | 2.19 | 3.33* | 929 | 3034 | 3197 | 6493 |
| C. merolae 10D# | 16.73 | 22 | 859.1 | 54.81 | 4803 | 3980 | 33 | 33 | 56.57 | 56.57 | 0.5 | 0.0 | 1 | 1.01 | 883 | 2811 | 2832 | 6213 |
| C. merolae Soos | 12.33 | 35 | 567.5 | 54.33 | 4406 | 3574 | 34 | 34 | 54.84 | 54.26 | 9.4 | 2.9 | 1.06 | 1.1 | 886 | 2787 | 2823 | 6188 |
Table 2
Natural habitats of extant prokaryotes harboring the closest orthologs to Cyanidiales HGTs.
Numbers in brackets represent how many times HGT candidates from Cyanidiales shared monophyly with non-eukaryotic organisms; for example Proteobacteria were found in 53/96 of the OG monophylies. King…
| Kingdom | Phylogeny | Natural habitat of closest non-eukaryotic ortholog | ||||
|---|---|---|---|---|---|---|
| Division | Species | Habitat description | pH | Max. temp | Salt | |
| Bacteria | Proteobacteria (53) | Acidithiobacillus thiooxidans (4) | Mine drainage/Mineral ores | 2.0–2.5 | 30°C | ‘hypersaline’ |
| Carnimonas nigrificans (4) | Raw cured meat | 3.0 | 35°C | 8% NaCl | ||
| Methylosarcina fibrata (4) | Landfill | 5.0–9.0 | 37°C | 1% NaCl | ||
| Sphingomonas phyllosphaerae (3) | Phyllosphere of Acacia caven | na | 28°C | na | ||
| Gluconacetobacter diazotrophicus (3) | Symbiont of various plant species | 2.0–6.0 | na | ‘high salt’ | ||
| Gluconobacter frateurii (3) | na | na | na | na | ||
| Luteibacter yeojuensis (3) | River | na | na | na | ||
| Thioalkalivibrio sulfidiphilus (3) | Soda lake | 8.0–10.5 | 40°C | 15% total salts | ||
| Thiomonas arsenitoxydans (3) | Disused mine site | 3.0–8.0 | 30°C | ‘halophilic’ | ||
| Firmicutes (28) | Sulfobacillus thermosulfidooxidans (6) | Copper mining | 2.0–2.5 | 45°C | ‘salt tolerant’ | |
| Alicyclobacillus acidoterrestris (4) | Soil sample | 2.0–6.0 | 53°C | 5% NaCl | ||
| Gracilibacillus lacisalsi (3) | Salt lake | 7.2–7.6 | 50°C | 25% total salts | ||
| Actinobacteria (19) | Amycolatopsis halophila (3) | Salt lake | 6.0–8.0 | 45°C | 15% NaCl | |
| Rubrobacter xylanophilus (3) | Thermal industrial runoff | 6.0–8.0 | 60°C | 6.0% NaCl | ||
| Chloroflexi (12) | Caldilinea aerophila (4) | Thermophilic granular sludge | 6.0–8.0 | 65°C | 3% NaCl | |
| Ardenticatena maritima (3) | Coastal hydrothermal field | 5.5–8.0 | 70°C | 6% NaCl | ||
| Ktedonobacter racemifer (3) | Soil sample | 4.8–6.8 | 33°C | >3% NaCl | ||
| Bacteroidetes Chlorobi (10) | Salinibacter ruber (4) | Saltern crystallizer ponds | 6.5–8.0 | 52°C | 30% total salts | |
| Salisaeta longa (3) | Experimental mesocosm (Salt) | 6.5–8.5 | 46°C | 20% NaCl | ||
| Nitrospirae (7) | Leptospirillum ferriphilum (4) | Arsenopyrite biooxidation tank | 0–3.0 | 40°C | 2% NaCl | |
| Fibrobacteres (6) | Acidobacteriaceae bacterium TAA166 (3) | na | na | na | na | |
| Deinococcus (5) | Truepera radiovictrix (3) | Hot spring runoffs | 7.5–9.5 | na | 6% NaCl | |
| Archaea | Euryarchaeota (6) | Ferroplasma acidarmanus (3) | Acid mine drainage | 0–2.5 | 40°C | ‘halophilic’ |
Appendix 1—table 1
Sequencing and Assembly stats.
The strains were sequenced using PacBio’s RS2 sequencing technology and P6-C4 chemistry (the only exception being C. merolae Soos, which was sequenced using P4-C2 chemistry). For genome assembly, …
| Species | Raw reads | Raw reads N50 | Raw reads GC | Raw reads (bp) | Raw reads coverage | Unitigging (bp) | Unitigging coverage | Genome size (bp) | Genome GC | Contigs | Contig N50 | Genes | Busco (C) | Busco (C + F) | Busco (D) | Busco (M) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| G. sulphuraria RT22 | 163764 | 12023 | 35.83% | 1424372481 | 91.20 | 1108677098 | 70.99 | 15617852 | 37.43% | 118 | 172878 | 6982 | 92.8% | 94.5% | 6.3% | 5.5% |
| G. sulphuraria 002 | 131978 | 10109 | 37.90% | 946093501 | 67.05 | 805608410 | 57.09 | 14110219 | 39.16% | 107 | 189293 | 5912 | 87.5% | 92.5% | 5.0% | 7.5% |
| G. sulphuraria 5572 | 101472 | 10449 | 36.45% | 802203307 | 56.19 | 664626554 | 46.55 | 14277368 | 37.99% | 108 | 229711 | 6472 | 91.5% | 93.5% | 5.0% | 6.5% |
| G. sulphuraria MS1 | 128294 | 9991 | 36.18% | 934546621 | 62.77 | 777587876 | 52.23 | 14887946 | 37.62% | 129 | 172087 | 7441 | 90.8% | 94.1% | 4.0% | 5.9% |
| G. sulphuraria MtSh | 158936 | 13617 | 39.19% | 1523875693 | 101.95 | 1235394614 | 82.65 | 14947614 | 40.04% | 101 | 186619 | 6160 | 87.4% | 91.7% | 6.9% | 8.3% |
| G. sulphuraria Azora | 82544 | 10244 | 37.09% | 651280930 | 46.31 | 551720524 | 39.23 | 14063793 | 40.10% | 127 | 162248 | 6305 | 88.4% | 92.0% | 2.3% | 8.0% |
| G. sulphuraria SAG21.92 | 71480 | 10341 | 36.67% | 564874149 | 39.47 | 413793659 | 28.91 | 14312824 | 37.92% | 135 | 158217 | 5956 | 83.8% | 88.4% | 3.6% | 11.6% |
| G. sulphuraria YNP5587.1 | 77421 | 13842 | 36.69% | 769606723 | 53.38 | 613905250 | 42.58 | 14416547 | 40.05% | 115 | 170797 | 6118 | 91.8% | 93.5% | 5.0% | 6.5% |
| G. phlegrea Soos | 92263 | 14365 | 36.01% | 966702049 | 65.00 | 619580741 | 41.66 | 14872696 | 37.52% | 108 | 201071 | 6125 | 92.1% | 93.8% | 7.9% | 6.2% |
| C. merolae Soos | 154461 | 7924 | 52.92% | 848542698 | 68.82 | 570542830 | 46.27 | 12329961 | 54.33% | 35 | 567466 | 4406 | 85.2% | 89.5% | 2.0% | 10.5% |
| G. sulphuraria074W* | 13712004 | 36.89% | 433 | 172322 | 7177 | 83.8% | 87.4% | 2.3% | 10.3% | |||||||
| C. merolae 10D* | 16728945 | 54.81% | 22 | 859119 | 5044 | 90.4% | 93.4% | 1.3% | 6.6% | |||||||
| G. phlegrea DBV009* | 11413183 | 37.86% | 9311 | 1993 | 7836 | 68.3% | 88.1% | 3.6% | 11.9% |
Appendix 3—table 1
%GC analysis of the Cyanidiales transcriptomes.
%GC content of HGT genes was compared to the %GC content of native genes using students test. Legend: HGT Genes: number of HGT gene candidates found in species. Avg. %GC Native: average %GC of …
| HGT genes | Avg. %GC Native | Avg. %GC HGT | p-Val (T-test) | Delta | |
|---|---|---|---|---|---|
| Galdieria_sulphuraria_074W | 55 | 38.99 | 39.62 | 0.046 | 0.63 |
| Galdieria_sulphuraria_MS1 | 58 | 39.59 | 40.79 | 0 | 1.2 |
| Galdieria_sulphuraria_RT22 | 54 | 39.54 | 40.85 | 0 | 1.31 |
| Galdieria_sulphuraria_SAG21 | 47 | 40.04 | 41.47 | 0 | 1.43 |
| Galdieria_sulphuraria_MtSh | 47 | 41.33 | 42.48 | 0 | 1.15 |
| Galdieria_sulphuraria_Azora | 58 | 41.34 | 42.57 | 0 | 1.23 |
| Galdieria_sulphuraria_YNP55871 | 46 | 41.33 | 42.14 | 0.006 | 0.81 |
| Galdieria_sulphuraria_5572 | 53 | 39.68 | 40.5 | 0.002 | 0.82 |
| Galdieria_sulphuraria_002 | 52 | 40.76 | 41.35 | 0.016 | 0.59 |
| Galdieria_phlegrea_DBV08 | 54 | 39.97 | 40.58 | 0.016 | 0.61 |
| Galdieria_phlegrea_Soos | 44 | 39.57 | 40.73 | 0 | 1.16 |
| Cyanidioschyzon_merolae_10D | 33 | 56.57 | 56.57 | 0.996 | 0 |
| Cyanidioschyzon_merolae_Soos | 34 | 54.84 | 54.26 | 0.479 | −0.58 |
Appendix 4—table 1
Single exon genes vs multiexonic.
The ratio of single exon genes vs multiexonic genes was compared between HGT candidates and native Cyanidiales genes (Fisher enrichment test). Legend: HGT Genes: number of HGT gene candidates found …
| HGT genes | Single exon (HGT) | Multi exon (HGT) | Single exon (Native) | Multi exon (Native) | Fisher's p | Single exon % (HGT) | Single exon % (Native) | Multi exon % (HGT) | Multi exon % (Native) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Galdieria_sulphuraria_074W | 55 | 29 | 26 | 1879 | 5240 | 4.05E-05 | 52.7% | 26.4% | 47.3% | 73.6% |
| Galdieria_sulphuraria_MS1 | 58 | 22 | 36 | 1224 | 6159 | 0.0001098 | 37.9% | 16.6% | 62.1% | 83.4% |
| Galdieria_sulphuraria_RT22 | 54 | 26 | 28 | 1756 | 5172 | 0.0004079 | 48.1% | 25.3% | 51.9% | 74.7% |
| Galdieria_sulphuraria_SAG21 | 47 | 8 | 39 | 901 | 5008 | 0.6852 | 17.0% | 15.2% | 83.0% | 84.8% |
| Galdieria_sulphuraria_MtSh | 47 | 17 | 30 | 1239 | 4874 | 0.01054 | 36.2% | 20.3% | 63.8% | 79.7% |
| Galdieria_sulphuraria_Azora | 58 | 14 | 39 | 966 | 5286 | 0.03558 | 24.1% | 15.5% | 75.9% | 84.5% |
| Galdieria_sulphuraria_YNP55871 | 46 | 21 | 25 | 1548 | 4524 | 0.00341 | 45.7% | 25.5% | 54.3% | 74.5% |
| Galdieria_sulphuraria_5572 | 53 | 29 | 24 | 1389 | 5030 | 1.75E-07 | 54.7% | 21.6% | 45.3% | 78.4% |
| Galdieria_sulphuraria_002 | 52 | 26 | 26 | 140 | 4720 | 8.75E-07 | 50.0% | 2.9% | 50.0% | 97.1% |
| Galdieria_phlegrea_DBV009 | 54 | na | na | na | na | na | na | na | na | na |
| Galdieria_phlegrea_Soos | 44 | 25 | 22 | 1369 | 4709 | 5.17E-06 | 56.8% | 22.5% | 43.2% | 77.5% |
| Cyanidioschyzon_merolae_ 10D | 33 | 33 | 0 | 4744 | 26 | 1 | 100.0% | 99.5% | 0.0% | 0.5% |
| Cyanidioschyzon_merolae_Soos | 34 | 33 | 1 | 3960 | 412 | 0.367 | 97.1% | 90.6% | 2.9% | 9.4% |
Appendix 4—table 2
Exon/Gene ratio.
The ratio of exons per gene was compared between HGT candidates and native Cyanidiales genes (Wilcox ranked test). Legend: HGT Genes: number of HGT gene candidates found in species. E/G All: average …
| HGT genes | Mean exon per transcript (HGT) | Mean exon per transcript (Native) | Wilcox (p) | Delta | |
|---|---|---|---|---|---|
| Galdieria_sulphuraria_074W | 55 | 2.25 | 3.2 | 9.40E-06 | 0.95 |
| Galdieria_sulphuraria_MS1 | 58 | 2.5 | 3.88 | 1.41E-05 | 1.38 |
| Galdieria_sulphuraria_RT22 | 54 | 2.63 | 3.95 | 3.42E-06 | 1.32 |
| Galdieria_sulphuraria_SAG21 | 47 | 4.02 | 5.03 | 0.0004 | 1.01 |
| Galdieria_sulphuraria_MtSh | 47 | 3.15 | 4.32 | 0.0011 | 1.17 |
| Galdieria_sulphuraria_Azora | 58 | 2.68 | 4.03 | 9.92E-05 | 1.35 |
| Galdieria_sulphuraria_YNP55871 | 46 | 2.61 | 3.65 | 2.30E-04 | 1.04 |
| Galdieria_sulphuraria_5572 | 53 | 2.15 | 3.53 | 2.25E-07 | 1.38 |
| Galdieria_sulphuraria_002 | 52 | 2.37 | 3.73 | 2.65E-06 | 1.36 |
| Galdieria_phlegrea_DBV009 | 54 | na | na | na | na |
| Galdieria_phlegrea_Soos | 44 | 2.19 | 3.33 | 1.19E-05 | 1.14 |
| Cyanidioschyzon_merolae_10D | 33 | 1 | 1.01 | 1.00E + 00 | 0.01 |
| Cyanidioschyzon_merolae_Soos | 34 | 1.06 | 1.1 | 2.10E-01 | 0.04 |
Additional files
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Transparent reporting form
- https://doi.org/10.7554/eLife.45017.107
