Genomics analysis of the light-harvesting chlorophyll a/b-binding (Lhc) superfamily in cassava (Manihot esculenta Crantz)

The light-harvesting chlorophyll a/b-binding (Lhc) superfamily, composed of several distinct antennae protein families, plays essential roles in light capture and photoprotection in plants. Compared with the extensive research in Arabidopsis thaliana and certain species, little is known about this superfamily in cassava (Manihot esculenta), an Euphorbiaceous plant experienced one so-called rho recent whole-genome duplication (WGD). This study presents the first genome-wide identification of Lhc supergene family in cassava, resulting in 35 members that are distributed across 15 chromosomes. Phylogenetic analysis and BRH (Best Reciprocal Hit)-based sequence comparison assigned these genes into four previously defined families and 26 orthologous groups (including one absent from Arabidopsis). Synteny analysis showed that nine identified duplicates were derived from the WGD as well as local duplication, and retention bias of WGD duplicates in this species was shown to be something different from that in Arabidopsis which experienced two recent WGDs. Transcriptional profiling of MeLhc superfamily genes revealed a predominant expression pattern in green tissues such as leaf and midvein. Moreover, comparison of exon-intron structures, protein motifs, and gene expression profiles revealed divergence of duplicate pairs. Our findings will not only improve our knowledge on the evolution of this superfamily in cassava, but also provide valuable information for further functional studies.