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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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Related in: MedlinePlus

17-mer frequency percentage distribution curve of sequencing reads of diploid L. striatellus (A) and M. cingulum(B). The X-axis represents the sequencing depth (X), and the Y-axis represents the proportion of specific k-mers to the total k-mer numbers with a giving sequencing depth. For L. striatellus, the 17-mer depth distribution graph shows a low level of heterozygosity and the genome size of L. striatellus was estimated to be 657 Mb. For M. cingulum, the k-mer depth distributions with a minor peak indicate a relatively low level of heterozygosity (0.4%) and the genome size was estimated to be 136 Mb.
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Figure 2: 17-mer frequency percentage distribution curve of sequencing reads of diploid L. striatellus (A) and M. cingulum(B). The X-axis represents the sequencing depth (X), and the Y-axis represents the proportion of specific k-mers to the total k-mer numbers with a giving sequencing depth. For L. striatellus, the 17-mer depth distribution graph shows a low level of heterozygosity and the genome size of L. striatellus was estimated to be 657 Mb. For M. cingulum, the k-mer depth distributions with a minor peak indicate a relatively low level of heterozygosity (0.4%) and the genome size was estimated to be 136 Mb.

Mentions: The k-mer analysis was used to estimate the genome sizes of L. striatellus and M. cingulum using Illumina Solexa sequencing data. The 17-mer depth distributions showed a single peak, indicating that both insects had very low heterogeneity. Based on k-mer analysis, the genome size of L. striatellus was 657 Mb and that of M. cingulum was 136 Mb (Figure 2). These values were slightly different from estimates made using flow cytometry. This difference might be due to the variability of the two methods. Another possible reason was that different samples were used for the k-mer analysis. If this is the case, the genome size differences between different samples require further investigation. Regardless, it still can be concluded that L. striatellus had a moderate-size genome of 500–700 Mb while M. cingulum had a small-size genome of ~150 Mb. The exact genome size requires confirmation by additional genome-sequencing.


Genome Sizes of Nine Insect Species Determined by Flow Cytometry and k -mer Analysis
17-mer frequency percentage distribution curve of sequencing reads of diploid L. striatellus (A) and M. cingulum(B). The X-axis represents the sequencing depth (X), and the Y-axis represents the proportion of specific k-mers to the total k-mer numbers with a giving sequencing depth. For L. striatellus, the 17-mer depth distribution graph shows a low level of heterozygosity and the genome size of L. striatellus was estimated to be 657 Mb. For M. cingulum, the k-mer depth distributions with a minor peak indicate a relatively low level of heterozygosity (0.4%) and the genome size was estimated to be 136 Mb.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121235&req=5

Figure 2: 17-mer frequency percentage distribution curve of sequencing reads of diploid L. striatellus (A) and M. cingulum(B). The X-axis represents the sequencing depth (X), and the Y-axis represents the proportion of specific k-mers to the total k-mer numbers with a giving sequencing depth. For L. striatellus, the 17-mer depth distribution graph shows a low level of heterozygosity and the genome size of L. striatellus was estimated to be 657 Mb. For M. cingulum, the k-mer depth distributions with a minor peak indicate a relatively low level of heterozygosity (0.4%) and the genome size was estimated to be 136 Mb.
Mentions: The k-mer analysis was used to estimate the genome sizes of L. striatellus and M. cingulum using Illumina Solexa sequencing data. The 17-mer depth distributions showed a single peak, indicating that both insects had very low heterogeneity. Based on k-mer analysis, the genome size of L. striatellus was 657 Mb and that of M. cingulum was 136 Mb (Figure 2). These values were slightly different from estimates made using flow cytometry. This difference might be due to the variability of the two methods. Another possible reason was that different samples were used for the k-mer analysis. If this is the case, the genome size differences between different samples require further investigation. Regardless, it still can be concluded that L. striatellus had a moderate-size genome of 500–700 Mb while M. cingulum had a small-size genome of ~150 Mb. The exact genome size requires confirmation by additional genome-sequencing.

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.

No MeSH data available.


Related in: MedlinePlus