Plant protein-coding gene families: Their origin and evolution

Abstract

Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.

Keywords: gene duplication; gene families; gene loss; molecular evolution; plant evolution.

FIGURE 1

Plant evolution. The symbiosis of dinoflagellate protists with cyanobacteria prompted the occurrence of phytoplanktonic communities, with diverse phytoplanktonic taxa (including plants, green algae, red algae, and cryptophytes) arising through biological adaptation to the environment. At the origin of green algae and Streptophytina, significant differences in drought and oxygen stress tolerance developed to facilitate terrestrialization. During the process of adaptation to the environment, certain taxa underwent unique adaptations in root, flower, and other related phenotypes, which in turn ensured the dominance of the widely distributed angiosperms.

FIGURE 2

Plant gene families. (A) A brief classification of gene families found in plants. (B) A rich taxonomy of plant transcription factors. tRNA is an RNA composed of 76–90 nucleotides that carry amino acids into the ribosome and synthesize proteins under the guidance of mRNA; lnc RNA is a class of non-coding RNA molecules longer than 200 nt; mi RNA is a class of endogenous, small RNAs of about 20–24 nucleotides in length; circ RNA is a class of RNAs that do not have a 5′ terminal cap and 3′ terminal poly(A) tail, and are covalently bonded to form a loop structure; they are a class of non-coding RNA molecules that are found in living organisms. cnc RNA (coding and non-coding RNA) is a family of functional genes that can be differentially sheared in a variable manner, resulting in both short peptides or small molecular weight proteins and untranslatable functional RNAs (e.g., Inc RNA, mi RNA, etc.).

FIGURE 3

Origin and expansion of plant gene families. Gene families in boxes representing their origin in green algae or earlier. Families include OPR (12-oxo-phytodienoate acid reductase), KCS (3-ketoacyl-coa synthase), AGO (Argonaute), TLP (thaumatin-like protein), NBS-LRR (nucleotide binding site leucine-rich repeat), ALOG (Arabidopsis LSH1 and Oryza G1), WOX (WUSCHEL-related), C3HDZ (class III homeodomain-zinc finger protein), 3R-MYB, PFDN (prefoldin), AOX (alternative oxidase), SH3P (SH3 and BAR domain-containing protein), CesA (cellulose synthase), FT/TFL1 (flowering locus t/terminal flower 1), Myo (myosin), Cyc (cyclin), AQP (aquaporins), DLC (dynein light chain), GPAT (glycerol-3-phosphate acyltransferase), VP (vacuolar-type H+-pyrophosphatase), PHO (phosphate 1), CIMS (cobalamin-independent methionine synthase), and FBP (F-box). Gene families listed in the star may have contributed to the development of Streptophyte algae or functional innovations in the plant community, and include AHL (AT-hook motif nuclear localized), HMGR (3-hydroxy-3-methylglutaryl coenzyme A reductase), Aux/IAA (auxin/indole acetic acid and auxin response factor), HAM (hairy meristem), and OFP (OVATE family protein).