Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Abstract

The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber, fruit and nut industry. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for it. The genome size of B. horsfieldi was estimated as approximate 520 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.26% and 51.03%, respectively. The assembled genome was 528.56Mb with GC content of 35.40%. A total of 121750 microsatellite motifs were identified. The most frequent repeat motif was mononucleotide with a frequency of 85.84%, followed by 8.08% of dinonucleotide, 5.04% of trinonucleotide, 0.73% of tetranonucleotide, 0.20% of pentanonucleotide and 0.12% of hexanonucleotide motifs. The AT/AT, TA/TAand GA/TC repeats were the most abundant motifs of dinucleotide motifs, and AAT/ATT, TAA/TTA and ATA/TAT were the most abundant motifs of trinucleotide motifs, respectively. ninety six pairs of SSR primers were randomly selected for PCR amplification and agarose gel electrophoresis detection, among which 56 pairs of primers can be effectively amplified to obtain the target fragment. In summary, various candidate microsatellite markers were identified and characterized in this study using genome survey analysis.

Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops

“…Of tetra-, penta-, and hexanucleotide SSRs, (AAAT) n , (AAAG) n , (AAACC) n , (AAATC) n , (AAATT) n , (AATAT) n , (AATCT) n , (ACATAT) n , and (AAATTC) n were the more frequent motifs. Overall, these findings are consistent with previous reports suggesting that AT-rich SSR motifs predominate [ 43 , 48 ]. The abundance of AT-rich SSRs might also reflect the overall base composition of insect genomes, which are often AT-rich themselves [ 43 ].…”

“…More specifically, we observed dinucleotide SSRs to be the most frequent repeat type in R. ferrugineus and I. nitidus , consistent with dicotyledons [ 47 ] and Drosophila [ 14 ]. Mononucleotide SSRs were the dominant type in S. oryzae , P. strobi , L. oregonensis , and L. bonariensis , which is consistent with prior findings for Batocera horsfieldi [ 48 ] and eukaryotic genomes [ 39 , 49 ]. Finally, trinucleotide SSRs were the most abundant type in H. hampei , which is consistent with eukaryotes [ 50 ].…”