Phytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions

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Science Advances  29 Apr 2020:
Vol. 6, no. 18, eaba0111
DOI: 10.1126/sciadv.aba0111
  • Fig. 1 Summary of prokaryotic-derived HGTs in 23 CRASH taxa.

    The bar plot indicates the amount of HGT detected in each species, with the black bar representing gene counts, and the pink bar, gene families. The red “M” and green “S” indicate multicellular and unicellular taxa, respectively.

  • Fig. 2 Putative origins of HGTs in CRASH taxa and phenotypes of HGT donors.

    (A) Maximum likelihood tree of pantothenate kinase genes (left) and the two scenarios to explain the phylogeny (right). The simplified tree of life includes Cryptophyta (C), Rhizaria (R), Alveolata (A), stramenopiles (S), Haptophyta (H), Archaeplastida (Ar), Excavata (Ex), Amoebozoa/Opisthokonta/Fungi (A/O/F), and Bacteria/Archaea (B/Ac). Red crosses on the branches indicate putative gene losses in the tree. The dashed arrow marks the direction of gene transfer. (B) MMSH-based inference of HGT donors. Prokaryote phylogeny (left) was retrieved from the NCBI taxonomy database. The total HGT counts for each donor phylum (row) are shown as a bar plot (right edge). The TACK group includes Thaumarchaeota, Aigarchaeota, Chrenarchaeota and Korarcheaota. (C) MMSH-based phenotype of HGT donors. The phenotype data were retrieved from the NCBI microbial attributes database. The dominant types are indicated.

  • Fig. 3 Examples of HGTs that occurred in limited CRASH species.

    (A) Maximum likelihood tree of efflux MFS transporter Tet(C) gene. (B) Maximum likelihood tree of BchC. The inference of gene loss under the HGT and differential loss scenarios are as in Fig. 2. Eukaryotic sequences from CRASH are marked in orange, whereas the others are marked in gray.

  • Fig. 4 Gene structure and functional annotation of HGTs.

    (A) The smaller CDS length in HGTs than in core genes is shown. The bar plots in blue, red, and gray indicate CRASH host core genes, HGTs, and their corresponding MMSH in prokaryotes, respectively. Each dot in the boxplot charts indicates the mean value for a CRASH species. Lines connect the same species across bar plots, with green color indicating decreases in value from left to right and red color indicating increases in value. The dots along the central vertical lines of bar plots are colored differentially for stramenopiles (brown), Alveolata (red), Rhizaria (blue), Haptophyta (green), and Cryptophyta (purple). (B) The lower gene density in genomic regions flanking HGTs than in CRASH core genes is shown. The 100 kbp upstream and downstream were surveyed in all 23 CRASH species; red line represents gene density of HGTs, whereas the blue line is for core genes. Every point stands for the average count of genes in the 10k length bin, using all data from 23 species. (C) The higher frequency of single-exon genes in HGTs than in core genes is shown. (D) Here, the lower intron number per gene in intron-bearing HGTs than in core genes is shown. The combined data from 23 CRASH species are shown as the blue dots. (E) The functional divergence of HGTs. Splits tree of 23 CRASH lineages based on the novel functions acquired in each lineage via HGT. The dashed lines connect gene functions present in two or more lineages. (F) Functional enrichment of HGTs. Only significantly enriched GO terms (P < 0.05 after multitest correction) are included. The probability value and fold change are indicated by the colors and circle sizes. **P < 0.001.

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