Limits...
Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.

Rius N, Guillén Y, Delprat A, Kapusta A, Feschotte C, Ruiz A - BMC Genomics (2016)

Bottom Line: We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes.However, TEs alone do not explain the genome size difference.We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models.

View Article: PubMed Central - PubMed

Affiliation: Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain. nuria.rius.camps@gmail.com.

ABSTRACT

Background: Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis.

Results: We have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of the D. buzzatii st-1 genome is made up of TEs, between 7 and 7,5 % of D. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes.

Conclusions: TEs in D. buzzatii are less abundant than in D. mojavensis, as expected according to the genome size and TE content positive correlation. However, TEs alone do not explain the genome size difference. TEs accumulate in the dot chromosomes and proximal regions of D. buzzatii and D. mojavensis chromosomes. We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families in D. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy.

No MeSH data available.


Order correction. Main order contribution (kb) to D. buzzatii st-1 genome, before (blue) and after (red) the coverage-based correction
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4862133&req=5

Fig4: Order correction. Main order contribution (kb) to D. buzzatii st-1 genome, before (blue) and after (red) the coverage-based correction

Mentions: Consequently, the orders and superfamilies with a higher correction factor are the ones with copies missing in the assembly. The results (Fig. 4 and Table 1) show that LTR-retrotransposons are the most underestimated order in D. buzzatii st-1 annotation by a factor of 1.98. At the superfamily level (Fig. 5), Gypsy and BelPao are the most underestimated in D. buzzatii st-1 annotation, increasing after the correction by more than two fold.Fig. 4


Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.

Rius N, Guillén Y, Delprat A, Kapusta A, Feschotte C, Ruiz A - BMC Genomics (2016)

Order correction. Main order contribution (kb) to D. buzzatii st-1 genome, before (blue) and after (red) the coverage-based correction
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4862133&req=5

Fig4: Order correction. Main order contribution (kb) to D. buzzatii st-1 genome, before (blue) and after (red) the coverage-based correction
Mentions: Consequently, the orders and superfamilies with a higher correction factor are the ones with copies missing in the assembly. The results (Fig. 4 and Table 1) show that LTR-retrotransposons are the most underestimated order in D. buzzatii st-1 annotation by a factor of 1.98. At the superfamily level (Fig. 5), Gypsy and BelPao are the most underestimated in D. buzzatii st-1 annotation, increasing after the correction by more than two fold.Fig. 4

Bottom Line: We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes.However, TEs alone do not explain the genome size difference.We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models.

View Article: PubMed Central - PubMed

Affiliation: Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain. nuria.rius.camps@gmail.com.

ABSTRACT

Background: Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis.

Results: We have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of the D. buzzatii st-1 genome is made up of TEs, between 7 and 7,5 % of D. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes.

Conclusions: TEs in D. buzzatii are less abundant than in D. mojavensis, as expected according to the genome size and TE content positive correlation. However, TEs alone do not explain the genome size difference. TEs accumulate in the dot chromosomes and proximal regions of D. buzzatii and D. mojavensis chromosomes. We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families in D. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy.

No MeSH data available.