Comparative cytogenetics and derived phylogenic relationship among Sitophilus grain weevils (Coleoptera, Curculionidae, Dryophthorinae)

Abstract

Cytogenetic characteristics and genome size are powerful tools for species characterization and identification of cryptic species, providing critical insights into phylogenetic and evolutionary relationships. Sitophilus Linnaeus, 1758 grain weevils can benefit from such tools as key pest species of stored products and also as sources of archeological information on human history and past urban environments. Moreover, the phylogenetic relationship among these weevil species remains controversial and is largely based on single DNA fragment analyses. Therefore, cytogenetic analyses and genome size determinations were performed for four Sitophilus grain weevil species, namely the granary weevil Sitophilus granarius (Linnaeus, 1758), the tamarind weevil S. linearis (Herbst, 1797), the rice weevil S. oryzae (Linnaeus, 1763), and the maize weevil S. zeamais Motschulsky, 1855. Both maize and rice weevils exhibited the same chromosome number (2n=22; 10 A + Xyp). In contrast, the granary and tamarind weevils exhibited higher chromosome number (2n=24; 11 A + Xyp and 11 A + neo-XY, respectively). The nuclear DNA content of these species was not proportionally related to either chromosome number or heterochromatin amount. Maize and rice weevils exhibited similar and larger genome sizes (0.730±0.003 pg and 0.786±0.003 pg, respectively), followed by the granary weevil (0.553±0.003 pg), and the tamarind weevil (0.440±0.001 pg). Parsimony phylogenetic analysis of the insect karyotypes indicate that S. zeamais and S. oryzae were phylogenetically closer than S. granarius and S. linearis, which were more closely related and share a more recent ancestral relationship.

Diversity and convergence of mechanisms involved in pyrethroid resistance in the stored grain weevils, Sitophilus spp.

“…However, the absence of the L1014F mutation among Brazilian maize weevils is intriguing. Although both weevil species have overlapping distributions in southern part of Brazil and are subjected to similar selection pressures 29 , their evolutive and demographic histories are independents as the two weevil species split around 8.5 million years ago 30 , 31 , suggesting that the mutations based resistance in the Sitophilus species was generated by independent evolution events.…”

“…However, this single mutation alone does not explain the high levels of resistance observed in maize weevil strains, and therefore, additional effort is required to understand the molecular basis of the resistance mechanisms involved in this species. The rice weevil is the subject of even greater neglect but also deserves attention because of the importance as a pest species and the relatively close phylogenetic relationship with the maize weevil 29 – 31 . Besides the resistance to insecticides resulting from the target site and metabolic alterations, other mechanisms associated with behavioral modification such as change in locomotory parameters have been reported in aphids 32 and Sitophilus spp.…”

The transposable element-rich genome of the cereal pest Sitophilus oryzae

“…The assembly pipeline was defined to optimize multiple criteria including gene completeness (BUSCO scores [ 50 ]) and reference-free metrics (number of contigs, total length, N50, number of N’s per 100 kbp and the proportion of shared 100-mers between the assembly and short reads). The karyotype of S. oryzae comprises 22 chromosomes [ 51 ], and the genome assembly consists of 2025 scaffolds spanning 770 Mbp with a N50 of 2.86 Mbp, demonstrating a high contiguity compared to other Coleopteran genomes (Table 1 ). The assembly size is consistent with the genome size measured through flow cytometry (769 Mbp in females and 768 Mbp in males [ 51 ]).…”

The transposable element-rich genome of the cereal pestSitophilus oryzae

“…We have sequenced and assembled the genome of the rice weevil S. oryzae at a base coverage depth of 142X using a combination of short and long read strategies (see Methods). The karyotype of S. oryzae comprises 22 chromosomes (Silva et al 2018), and the genome assembly consists of 2 025 scaffolds spanning 770 Mbp with a N50 of 2.86 Mbp, demonstrating a high contiguity compared to other Coleopteran genomes (Table 1). The assembly size is consistent with the genome size measured through flow cytometry (769 Mbp in females and 768 Mbp in males (Silva et al 2018)).…”

“…The karyotype of S. oryzae comprises 22 chromosomes (Silva et al 2018), and the genome assembly consists of 2 025 scaffolds spanning 770 Mbp with a N50 of 2.86 Mbp, demonstrating a high contiguity compared to other Coleopteran genomes (Table 1). The assembly size is consistent with the genome size measured through flow cytometry (769 Mbp in females and 768 Mbp in males (Silva et al 2018)). We assessed the completeness of the genome assembly using BUSCO (Seppey et al 2019) (97.9% complete and 0.7% fragmented), and along with the aforementioned statistics, S. oryzae is the best assembled Curculionidae genome to date (Keeling et al 2013; McKenna et al 2016; Tribolium Genome Sequencing Consortium et al 2008) (Table 1).…”