Expansion of three types of transposon superfamilies within 25 Mya lead to large genome size of a rice insect pest

Abstract

The brown planthoppers (BPH, Nilaparvata lugens), white backed planthopper (WBPH, Sogatella furcifera) and small brown planthopper (SBPH, Laodelphax striatellus) are widely distributed rice insect pests, causing huge annual yield loss of rice production. Though these three planthoppers belong to the same family, Delphacidae of Hemiptera, their genome sizes (GS) are very different, ranging from 541 to 1088 Mb. To uncover the main factors driving GS changes of three planthoppers, we first estimated the GS of their ancestor Fulgoroidea, to be 794.33 Mb, indicating GS expansion in BPH but contraction in SBPH and WBPH. Next, we identified repetitive sequences and compared the TE landscapes, showed that three types of transposon superfamilies, hAT, Tc1-Mariner and Gypsy, expanded within 25 Mya in BPH. In addition, BPH kept ancient TEs of Fulgoroidea dated back to 175 Mya, while SBPH and WBPH have lost most of these ancient TEs. Here, we present evidence that the gain of recently expanded TEs driving the GS expansion and loss of ancient TEs leading to the GS contraction, providing new insights into the mechanism of GS variation.