Carbon Flux and Carbohydrate Gene Families in Pineapple

The recently sequenced pineapple genome was used to identify and analyze some of the key gene families involved in carbohydrate biosynthesis, breakdown and modification. Gene products were grouped into glycosyltransferases (GT), glycoside hydrolases (GH), carbohydrate esterases (CE), and polysaccharide lyases (PL) based upon predicted catalytic activity. Non-catalytic carbohydrate-binding modules (CBM) and enzymes involved in lignification were also identified. The pineapple genes were compared with those from two and five monocot and eudicots species, respectively. The complement of pineapple sugar and cell wall metabolism genes is similar to that found in rice and sorghum, though the numbers of GTs and GHs is often fewer. This applies to a lesser extent to the genes involved in nucleotide-sugar interconversion, with both pineapple and papaya having a minimum complement. Interestingly, pineapple does not appear to contain mixed linkage β-glucan in its walls while possessing cellulose synthase-like (Csl), J and H genes. Pineapple and papaya have less than half the number of GT1 genes involved in small molecule glycosylation compared to Arabidopsis and tomato, and fewer members in GH families than Arabidopsis. The ratio of rice and sorghum to pineapple genes in GH families was more variable than in the case of GTs and it is unclear why pineapple GH gene numbers are so low. Rice, sorghum and pineapple have far fewer CE8, PL1 and GH28 genes related to pectin metabolism than most eudicots. The general lower number of cell wall genes in pineapple possibly reflects the absence of a genome duplication event. The data also suggests that pineapple straddles the boundary between grasses (family Poaceae) and eudicots in terms of genes involved in carbohydrate metabolism, which is also reflected in its cell wall composition.