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Genome Sizes of Nine Insect Species Determined by Flow Cytometry and k -mer Analysis

View Article: PubMed Central - PubMed

ABSTRACT

The flow cytometry method was used to estimate the genome sizes of nine agriculturally important insects, including two coleopterans, five Hemipterans, and two hymenopterans. Among which, the coleopteran Lissorhoptrus oryzophilus (Kuschel) had the largest genome of 981 Mb. The average genome size was 504 Mb, suggesting that insects have a moderate-size genome. Compared with the insects in other orders, hymenopterans had small genomes, which were averagely about ~200 Mb. We found that the genome sizes of four insect species were different between male and female, showing the organismal complexity of insects. The largest difference occurred in the coconut leaf beetle Brontispa longissima (Gestro). The male coconut leaf beetle had a 111 Mb larger genome than females, which might be due to the chromosome number difference between the sexes. The results indicated that insect invasiveness was not related to genome size. We also determined the genome sizes of the small brown planthopper Laodelphax striatellus (Fallén) and the parasitic wasp Macrocentrus cingulum (Brischke) using k-mer analysis with Illunima Solexa sequencing data. There were slight differences in the results from the two methods. k-mer analysis indicated that the genome size of L. striatellus was 500–700 Mb and that of M. cingulum was ~150 Mb. In all, the genome sizes information presented here should be helpful for designing the genome sequencing strategy when necessary.

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Flow cytometry estimation of the genome size for the sex specific insects. D. melanogaster was used as a reference standard and N. lugens and A. pisum were used as positive controls. The X-axis represents the relative fluorescence intensity of nuclei stained with propidium iodide in a nuclear suspension from head tissue. The Y-axis represents the number of nuclei. (A)L. oryzophilus females (981 Mb, 3C peak channel is 2028.59). (B)T. chinensis females (405 Mb, 2C peak channel is 205.86). (C)A. lucorum males (878 Mb, 2C peak channel is 446.71). (D)E. sophia females (372 Mb, 2C peak channel is 380.00). (E)B. longissima males (554 Mb, 2C peak channel is 763.58). (F)B. longissima females (443 Mb, 2C peak channel is 610.26). (G)L. striatellus males (458 Mb, 2C peak is channel 233.01). (H)L. striatellus females (555 Mb, 2C peak is channel 279.87). (I)S.‘furcifera males (657 Mb, 2C peak is channel 334.26). (J)S. furcifera females (734 Mb, 2C peak is channel 373.27). (K)C. livdipennis males (341 Mb, 2C peak is channel 173.45). (L)C. livdipennis females (354 Mb, 2C peak is channel 180.54). (M)M. cingulum males (161 Mb, 1C peak is channel 82.00). (N)M. cingulum females (157 Mb, 2C peak is channel 160.00). (O) Positive control N. lugens males (1077 Mb, 2C peak is channel 547.56). (P) Positive control N. lugens females (1226 mMb, 2C peak is channel 623.79). (Q) Mixed D. melanogaster males and females (176.4 Mb, 2C peak is channel 89.72). (R) Positive control A. pisum females (398 Mb, 2C peak is channel 434.00). The known genome size of positive control is 1137 Mb (N. lugens males), 1110 Mb (N. lugens females) and 464 Mb (A. pisum females), respectively.
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Figure 1: Flow cytometry estimation of the genome size for the sex specific insects. D. melanogaster was used as a reference standard and N. lugens and A. pisum were used as positive controls. The X-axis represents the relative fluorescence intensity of nuclei stained with propidium iodide in a nuclear suspension from head tissue. The Y-axis represents the number of nuclei. (A)L. oryzophilus females (981 Mb, 3C peak channel is 2028.59). (B)T. chinensis females (405 Mb, 2C peak channel is 205.86). (C)A. lucorum males (878 Mb, 2C peak channel is 446.71). (D)E. sophia females (372 Mb, 2C peak channel is 380.00). (E)B. longissima males (554 Mb, 2C peak channel is 763.58). (F)B. longissima females (443 Mb, 2C peak channel is 610.26). (G)L. striatellus males (458 Mb, 2C peak is channel 233.01). (H)L. striatellus females (555 Mb, 2C peak is channel 279.87). (I)S.‘furcifera males (657 Mb, 2C peak is channel 334.26). (J)S. furcifera females (734 Mb, 2C peak is channel 373.27). (K)C. livdipennis males (341 Mb, 2C peak is channel 173.45). (L)C. livdipennis females (354 Mb, 2C peak is channel 180.54). (M)M. cingulum males (161 Mb, 1C peak is channel 82.00). (N)M. cingulum females (157 Mb, 2C peak is channel 160.00). (O) Positive control N. lugens males (1077 Mb, 2C peak is channel 547.56). (P) Positive control N. lugens females (1226 mMb, 2C peak is channel 623.79). (Q) Mixed D. melanogaster males and females (176.4 Mb, 2C peak is channel 89.72). (R) Positive control A. pisum females (398 Mb, 2C peak is channel 434.00). The known genome size of positive control is 1137 Mb (N. lugens males), 1110 Mb (N. lugens females) and 464 Mb (A. pisum females), respectively.

Mentions: The genome sizes of the nine insect species, estimated by flow cytometry, are presented in Table 1. D. melanogaster was the external reference and N. lugens and A. pisum, with published genomes, were positive controls. All experiments were repeated at least two times and the results indicated that all replicates had good reproducibility. The estimated genome sizes of N. lugens were 1130 Mb for male and 1110 Mb for female. A. pisum was estimated to be 460 Mb, which was consistent with genome assembly results (Richards et al., 2010; Xue et al., 2014). Among the nine insects, L. oryzophilus had the largest genome size (981 Mb, 1.003 pg), which was approximately two-fold that of other Coleoptera B. longissimi (554 Mb for male and 443 Mb for female). The genome sizes of the other eight insects (omitting L. oryzophilus) were <1 Gb (the nucleic content ≤1 pg) and the average genome size was 504 Mb. These data indicate that the insects studied had a moderate genome size. Both S. furcifera and L. striatellus had a smaller genome size than N. lugens (Figure 1). The mirids C. livdipennis and T. chinensis had a genome size around 400 Mb but A. lucorum had a genome size of 878 Mb. Hymenoptera tend to have smaller genome sizes than other orders. The genome sizes of wasps in this study were <200 Mb with the exception of E. sophia, which had a larger genome size of 372 Mb.


Genome Sizes of Nine Insect Species Determined by Flow Cytometry and k -mer Analysis
Flow cytometry estimation of the genome size for the sex specific insects. D. melanogaster was used as a reference standard and N. lugens and A. pisum were used as positive controls. The X-axis represents the relative fluorescence intensity of nuclei stained with propidium iodide in a nuclear suspension from head tissue. The Y-axis represents the number of nuclei. (A)L. oryzophilus females (981 Mb, 3C peak channel is 2028.59). (B)T. chinensis females (405 Mb, 2C peak channel is 205.86). (C)A. lucorum males (878 Mb, 2C peak channel is 446.71). (D)E. sophia females (372 Mb, 2C peak channel is 380.00). (E)B. longissima males (554 Mb, 2C peak channel is 763.58). (F)B. longissima females (443 Mb, 2C peak channel is 610.26). (G)L. striatellus males (458 Mb, 2C peak is channel 233.01). (H)L. striatellus females (555 Mb, 2C peak is channel 279.87). (I)S.‘furcifera males (657 Mb, 2C peak is channel 334.26). (J)S. furcifera females (734 Mb, 2C peak is channel 373.27). (K)C. livdipennis males (341 Mb, 2C peak is channel 173.45). (L)C. livdipennis females (354 Mb, 2C peak is channel 180.54). (M)M. cingulum males (161 Mb, 1C peak is channel 82.00). (N)M. cingulum females (157 Mb, 2C peak is channel 160.00). (O) Positive control N. lugens males (1077 Mb, 2C peak is channel 547.56). (P) Positive control N. lugens females (1226 mMb, 2C peak is channel 623.79). (Q) Mixed D. melanogaster males and females (176.4 Mb, 2C peak is channel 89.72). (R) Positive control A. pisum females (398 Mb, 2C peak is channel 434.00). The known genome size of positive control is 1137 Mb (N. lugens males), 1110 Mb (N. lugens females) and 464 Mb (A. pisum females), respectively.
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Figure 1: Flow cytometry estimation of the genome size for the sex specific insects. D. melanogaster was used as a reference standard and N. lugens and A. pisum were used as positive controls. The X-axis represents the relative fluorescence intensity of nuclei stained with propidium iodide in a nuclear suspension from head tissue. The Y-axis represents the number of nuclei. (A)L. oryzophilus females (981 Mb, 3C peak channel is 2028.59). (B)T. chinensis females (405 Mb, 2C peak channel is 205.86). (C)A. lucorum males (878 Mb, 2C peak channel is 446.71). (D)E. sophia females (372 Mb, 2C peak channel is 380.00). (E)B. longissima males (554 Mb, 2C peak channel is 763.58). (F)B. longissima females (443 Mb, 2C peak channel is 610.26). (G)L. striatellus males (458 Mb, 2C peak is channel 233.01). (H)L. striatellus females (555 Mb, 2C peak is channel 279.87). (I)S.‘furcifera males (657 Mb, 2C peak is channel 334.26). (J)S. furcifera females (734 Mb, 2C peak is channel 373.27). (K)C. livdipennis males (341 Mb, 2C peak is channel 173.45). (L)C. livdipennis females (354 Mb, 2C peak is channel 180.54). (M)M. cingulum males (161 Mb, 1C peak is channel 82.00). (N)M. cingulum females (157 Mb, 2C peak is channel 160.00). (O) Positive control N. lugens males (1077 Mb, 2C peak is channel 547.56). (P) Positive control N. lugens females (1226 mMb, 2C peak is channel 623.79). (Q) Mixed D. melanogaster males and females (176.4 Mb, 2C peak is channel 89.72). (R) Positive control A. pisum females (398 Mb, 2C peak is channel 434.00). The known genome size of positive control is 1137 Mb (N. lugens males), 1110 Mb (N. lugens females) and 464 Mb (A. pisum females), respectively.
Mentions: The genome sizes of the nine insect species, estimated by flow cytometry, are presented in Table 1. D. melanogaster was the external reference and N. lugens and A. pisum, with published genomes, were positive controls. All experiments were repeated at least two times and the results indicated that all replicates had good reproducibility. The estimated genome sizes of N. lugens were 1130 Mb for male and 1110 Mb for female. A. pisum was estimated to be 460 Mb, which was consistent with genome assembly results (Richards et al., 2010; Xue et al., 2014). Among the nine insects, L. oryzophilus had the largest genome size (981 Mb, 1.003 pg), which was approximately two-fold that of other Coleoptera B. longissimi (554 Mb for male and 443 Mb for female). The genome sizes of the other eight insects (omitting L. oryzophilus) were <1 Gb (the nucleic content ≤1 pg) and the average genome size was 504 Mb. These data indicate that the insects studied had a moderate genome size. Both S. furcifera and L. striatellus had a smaller genome size than N. lugens (Figure 1). The mirids C. livdipennis and T. chinensis had a genome size around 400 Mb but A. lucorum had a genome size of 878 Mb. Hymenoptera tend to have smaller genome sizes than other orders. The genome sizes of wasps in this study were <200 Mb with the exception of E. sophia, which had a larger genome size of 372 Mb.

View Article: PubMed Central - PubMed

ABSTRACT

The flow cytometry method was used to estimate the genome sizes of nine agriculturally important insects, including two coleopterans, five Hemipterans, and two hymenopterans. Among which, the coleopteran Lissorhoptrus oryzophilus (Kuschel) had the largest genome of 981 Mb. The average genome size was 504 Mb, suggesting that insects have a moderate-size genome. Compared with the insects in other orders, hymenopterans had small genomes, which were averagely about ~200 Mb. We found that the genome sizes of four insect species were different between male and female, showing the organismal complexity of insects. The largest difference occurred in the coconut leaf beetle Brontispa longissima (Gestro). The male coconut leaf beetle had a 111 Mb larger genome than females, which might be due to the chromosome number difference between the sexes. The results indicated that insect invasiveness was not related to genome size. We also determined the genome sizes of the small brown planthopper Laodelphax striatellus (Fall&eacute;n) and the parasitic wasp Macrocentrus cingulum (Brischke) using k-mer analysis with Illunima Solexa sequencing data. There were slight differences in the results from the two methods. k-mer analysis indicated that the genome size of L. striatellus was 500&ndash;700 Mb and that of M. cingulum was ~150 Mb. In all, the genome sizes information presented here should be helpful for designing the genome sequencing strategy when necessary.

No MeSH data available.