Leaves are responsible for photosynthesis and transpiration and are highly diverse within the plant kingdom. Leaf development involves many gene families and is a very complex process, including the initiation of a leaf primordia and establishment of leaf polarity. Leaf development may depend heavily on the activities of homeodomain (HD) KNOTTED-like homeobox transcription factors (KNOX), which control the formation and maintenance of the shoot apical meristem. However, little is known about the features of KNOX genes across Viridiplantae, despite extensive studies within selected plant species.

Dr. GAO Jie of Xishuangbanna Tropical Botanical Garden (XTBG) and her collaborators carried out a systematic inventory of plant KNOX proteins in a total of 48 plant genomes, ranging from Chlorophyta to higher plants. They used available protein data and bioinformatics methods, including profile hidden Markov models (HMMs), to better understand the evolution of the KNOX gene family.

The study found that KNOX proteins were present in all investigated land plant species, as well as in specific phyla of green algae. In phylogenetic analyses, the KNOX proteins in green algae formed a distinct clade but were most similar to the class I KNOX proteins of land plants. Class II KNOX proteins were much more conserved in sequence than class I proteins and were likely under purifying selection. The KNOX genes have experienced two major events of expansion during the evolution of plants and specific plants are characterized by a dramatic increase in the number of KNOX paralogs.

To examine gene expression, the researchers made use of a large RNA-Seq dataset of Glycine max from a wide variety of tissues, 203 samples, and 346 sequencing runs. Consistent with previous studies, they observed for the higher plants that class II proteins had relatively broad tissue specificity, whereas class I proteins had a much more restricted distribution.

By using extensive dataset of the soybean Glycine max, it is possible to examine in detail tissue specificity and its relationship to the expansion of KNOX genes. The analysis of gene expression in G. max demonstrated that the expansion in gene number was associated with functional diversification.

The study entitled “Evolution, diversification, and expression of KNOX proteins in plants” has been published in Frontiers in Plant Science.