Fig 1.
Phylogenetic relationships among 24 land plant species and the distribution of NAC proteins identified in this study, based on the HMM-generated profile.
The total number of NAC proteins identified in each genome; the plant genome size, ploidy and chromosome number of each species; and the number of NAC sequences with Transmembrane motifs (TMM) for each genome are indicated on the right in colored squares. Ancient WGDs are represented by colored stars (details were taken from CoGepedia, https://genomevolution.org). Species names are color-coded as follows: blue–Moss, purple–pseudofern, red—monocots, and green—eudicots. * Genome size in Gb.
Fig 2.
Schematic representation of NAC OGs shared among Angiosperms.
A) Venn diagram showing the orthologous gene number shared between the P. patens outgroup and rice and grapevine genomes as the selected representatives for monocot and eudicot plants, respectively. The total overlap consisted of five proteins that define the basal core of the NAC genes. B) The number of orthologous proteins detected by means of BBH in 24 green plants. Green lines indicate the OGs shared between the moss P. paten, S. moellendorffii, and the basal taxa of the monocot and eudicot lineages. The number below the red line indicates the number of OGs shared between the rice and grapevine species. Black lines indicate the number of OGs shared among the monocots and eudicots with their respective selected pivotal species.
Fig 3.
Phylogenetic relationships of the NAC gene family.
A) Maximum likelihood phylogenetic tree derived from a MUSCLE alignment of the NAC domains from 24 plant species. The unrooted phylogenetic tree of the 2106 NAC proteins was clustered into six major families. Specific motifs found in the C-terminal region of the NAC proteins are shown next to each group. Blue lines and blue asterisks indicate sequences of P. patens in the tree, green circles show Arabidopsis proteins, and purple and red circles show grapevine and rice sequences, respectively. B) Schematic depiction of the proposed NAC family classification. Names of each subgroup are shown next to each clade. Triangles represent the NAC subgroups (detailed phylogenetic analysis is available in S4 Fig; branch lengths are arbitrary). C) Schematic representation of the five NAC's BOGs detected in the plant lineage and their affiliation into the major groups. Paralogous proteins for rice and grapevine are shown below each colored box. The affiliation of each BOG into the phylogenetic tree is available in S5C Fig) HMM LOGO of the NAC domain of 2106 proteins used in the phylogenetic tree.