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Table 1 Genes with evidence for positive selection in seagrasses

From: Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life

Branch Cluster ID Arabidopsis gene description p-value
LCA orthomcl1184 60 S ribosomal protein L14 (RPL14A) <0.001
LCA orthomcl3768 proteasome maturation factor UMP1 family protein 0.001
LCA orthomcl1461 annexin 7, calcium-dependent phospholipid binding (ANNAT7) 0.001
LCA orthomcl1674 cytochrome c oxidase 6B (COX6B) 0.002
LCA orthomcl538 chaperonin 20, calmodulin binding (CPN20) 0.003
LCA orthomcl4618 PSAE-1 0.004
LCA orthomcl5414 light harvesting complex PSII 5 (LHCB5) 0.004
LCA orthomcl1707 ubiquinol-cytochrome C reductase subunit, mitochondrial 0.005
LCA orthomcl3901 nuclear encoded CLP protease 5 (CLPP5) 0.006
LCA orthomcl1048 ferredoxin 3 (ATFD3) 0.007
LCA orthomcl4111 calmodulin binding (PSAN) 0.007
LCA orthomcl1171 protease inhibitor/seed storage/lipid transfer protein (LTP) 0.007
LCA orthomcl1074 60 S ribosomal protein L37 (RPL37A) 0.007
LCA orthomcl433 lipid transfer protein 3, lipid binding (LTP3) 0.008
LCA orthomcl1625 fructose-bisphosphate aldolase, putative 0.008
LCA orthomcl3789 PHD finger protein-related 0.009
LCA orthomcl801 60 S ribosomal protein L9 (RPL90B) 0.013
LCA orthomcl1693 UDP-D-apiose/UDP-D-xylose synthase 1 (AXS1) 0.016
LCA orthomcl1038 60 S ribosomal protein L18 (RPL18C) 0.020
LCA orthomcl922 glutaredoxin 4, metal ion binding (GRX4) 0.021
LCA orthomcl1070 60 S ribosomal protein L6 (RPL6B) 0.022
LCA orthomcl2948 scorbate peroxidase 4 (APX4) 0.025
LCA orthomcl1822 FK506 binding/peptidyl-prolyl cis-trans isomerase (FKBP15-2) 0.025
LCA orthomcl626 40 S ribosomal protein S3A (RPS3aB) 0.025
LCA orthomcl3845 copper ion bindng/electron carrier (DRT112) 0.026
LCA orthomcl1565 40 S ribosomal protein S15 (RPS15C) 0.028
LCA orthomcl4326 PQ-loop repeat family protein/transmembrane family protein 0.041
Po orthomcl469 copper ion binding/glutamate-ammninoa ligase (ATGSR1) <0.001
Po orthomcl1126 cytidylate kinase/uridylate kinase (PYR6) 0.001
Po orthomcl4752 glycine dehydrogenase, decarboxylating (GDCH) 0.002
Po orthomcl1625 fructose-bisphosphate aldolase, putative 0.003
Po orthomcl1125 40 S ribosomal protein S24 (RPS24B) 0.005
Po orthomcl1070 60 S ribosomal protein L6 (RPL6B) 0.007
Po orthomcl1673 cytochrome c-2 (CYTC-2) 0.008
Po orthomcl1473 C2 domain-containing protein 0.011
Po orthomcl1450 fructose-bisphosphate aldolase, putative 0.014
Po orthomcl824 mitochondrial ATP synthase g subunit family protein 0.014
Po orthomcl4197 enhancer of sos3-1, metal ion binding/protein binding (ENH1) 0.018
Po orthomcl4326 PQ-loop repeat family protein/transmembrane family protein 0.022
Po orthomcl1896 microsomal glutathione s-transferase, putative 0.028
Po orthomcl5121 frostbite 1, NADH dehydrogenase, ubiquinone (FRO1) 0.028
Po orthomcl2960 unknown protein 0.029
Po orthomcl1930 cornichon family protein 0.041
Po orthomcl433 lipid transfer protein 3, lipid binding (LTP3) 0.043
Po orthomcl1635 histone H1-3 (HIS1-3) 0.046
Zm orthomcl2446 photosystem I subunit L (PSAL) 0.001
Zm orthomcl1812 PS II subunit O-2, oxygen-evolving/poly(U) binding (PSBO2) 0.003
Zm orthomcl538 chaperonin 20, calmodulin binding (CPN20) 0.003
Zm orthomcl3901 nuclear encoded CLP protease 5 (CLPP5) 0.004
Zm orthomcl433 lipid transfer protein 3, lipid binding (LTP3) 0.005
Zm orthomcl414 structural constituent of ribosome 0.005
Zm orthomcl4111 calmodulin binding (PSAN) 0.007
Zm orthomcl591 RuBisCO activator (RCA) 0.008
Zm orthomcl1057 photosystem II subunit R (PSBR) 0.009
Zm orthomcl953 dormancy-associated protein-like 1 (DYL1) 0.010
Zm orthomcl3260 malate dehydrogenase, cytosolic, putative 0.012
Zm orthomcl1450 fructose-bisphosphate aldolase, putative 0.014
Zm orthomcl5948 prefoldin 6, unfolded protein binding (PDF6) 0.015
Zm orthomcl1565 40 S ribosomal protein S15 (RPS15C) 0.017
Zm orthomcl1808 universal stress protein (USP) family protein 0.031
Zm orthomcl824 mitochondrial ATP synthase g subunit family protein 0.032
Zm orthomcl4705 chlorophyll binding (LHCA3) 0.043
Zm orthomcl3845 copper ion bindng/electron carrier (DRT112) 0.044
Zm orthomcl4618 PSAE-1 0.045
Zm orthomcl3789 PHD finger protein-related 0.049
  1. Orthologous gene clusters with evidence for positive selection in at least one of the tested branches leading to Zostera marina (Zm), Posidonia oceanica (Po), and their last common ancestor (LCA; see Figure 1A). Each cluster was annotated using the TAIR9 functional description of the representative A. thaliana ortholog. P -values represent the significance of positive selection inferred by the branch-site test for positive selection.