The Juan non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity

<p>Abstract</p> <p>Background</p> <p>In contrast to DNA-mediated transposable elements (TEs), retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs), are generally considered to have a much lower propensity towards horizontal transfer. Detailed studies on site-specific non-LTR families have demonstrated strict vertical transmission. More studies are needed with non-site-specific non-LTR families to determine whether strict vertical transmission is a phenomenon related to site specificity or a more general characteristic of all non-LTRs. <it>Juan </it>is a Jockey clade non-LTR retrotransposon first discovered in mosquitoes that is widely distributed in the mosquito family <it>Culicidae</it>. Being a non-site specific non-LTR, <it>Juan </it>offers an opportunity to further investigate the hypothesis that non-LTRs are genomic elements that are primarily vertically transmitted.</p> <p>Results</p> <p>Systematic analysis of the ~1.3 Gbp <it>Aedes aegypti </it>(<it>Ae. aegypti</it>) genome sequence suggests that <it>Juan-A </it>is the only <it>Juan</it>-type non-LTR in <it>Aedes aegypti</it>. <it>Juan-A </it>is highly reiterated and comprises approximately 3% of the genome. Using minimum cutoffs of 90% length and 70% nucleotide (nt) identity, 663 copies were found by BLAST using the published <it>Juan-A </it>sequence as the query. All 663 copies are at least 95% identical to <it>Juan-A</it>, while 378 of these copies are 99% identical to <it>Juan-A</it>, indicating that the <it>Juan-A </it>family has been transposing recently in evolutionary history. Using the 0.34 Kb 5' UTR as the query, over 2000 copies were identified that may contain internal promoters, leading to questions on the genomic impact of <it>Juan-A</it>. <it>Juan </it>sequences were obtained by PCR, library screening, and database searches for 18 mosquito species of six genera including <it>Aedes</it>, <it>Ochlerotatus</it>, <it>Psorophora</it>, <it>Culex</it>, <it>Deinocerites</it>, and <it>Wyeomyia</it>. Comparison of host and <it>Juan </it>phylogenies shows overall congruence with few exceptions.</p> <p>Conclusion</p> <p><it>Juan-A </it>is a major genomic component in <it>Ae. aegypti </it>and it has been retrotransposing recently in evolutionary history. There are also indications that <it>Juan </it>has been recently active in a wide range of mosquito species. Furthermore, our research demonstrates that a Jockey clade non-LTR without target site-specificity has been sustained by vertical transmission in the mosquito family. These results strengthen the argument that non-LTRs tend to be genomic elements capable of persistence by vertical descent over a long evolutionary time.</p

The non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity-1

<p><b>Copyright information:</b></p><p>Taken from "The non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity"</p><p>http://www.biomedcentral.com/1471-2148/7/112</p><p>BMC Evolutionary Biology 2007;7():112-112.</p><p>Published online 9 Jul 2007</p><p>PMCID:PMC1947958.</p><p></p>Vg-C from is used to root the tree. Clade credibility values from 150,000 generations are given at each node. B. Consensus tree constructed with MrBayes using conceptually translated sequences of from PCR and genomic database (Aa, , Ag, ). Clade credibility values from 200,000 generations are given at each node or beside brackets. Ag-Jen-4 and other sequences correspond to families previously identified (Biedler and Tu 2003). Jockey elements from (Dm) and (Ct) are used to root the tree. Accessions are given beside sequence names. An asterisk indicates that the reading frame was intact. A bold capital "L" indicates that the sequence was obtained from a genomic library. The first three letters of a species name is used to label PCR and library sequences. Genus names are in bold beside brackets. is from and is from . Abbreviations: (); (); (); (); (); (); (); (); (); (); (); (); (); (); (); (); (). Number indicates clone from PCR. and sequences from genomic database (e.g. Ag-Jock-1, AaJockeyEle2) can be found in the TEfam database [57]. See additional files and for alignments used for phylogenetic inference

The non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity-3

<p><b>Copyright information:</b></p><p>Taken from "The non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity"</p><p>http://www.biomedcentral.com/1471-2148/7/112</p><p>BMC Evolutionary Biology 2007;7():112-112.</p><p>Published online 9 Jul 2007</p><p>PMCID:PMC1947958.</p><p></p>Vg-C from is used to root the tree. Clade credibility values from 150,000 generations are given at each node. B. Consensus tree constructed with MrBayes using conceptually translated sequences of from PCR and genomic database (Aa, , Ag, ). Clade credibility values from 200,000 generations are given at each node or beside brackets. Ag-Jen-4 and other sequences correspond to families previously identified (Biedler and Tu 2003). Jockey elements from (Dm) and (Ct) are used to root the tree. Accessions are given beside sequence names. An asterisk indicates that the reading frame was intact. A bold capital "L" indicates that the sequence was obtained from a genomic library. The first three letters of a species name is used to label PCR and library sequences. Genus names are in bold beside brackets. is from and is from . Abbreviations: (); (); (); (); (); (); (); (); (); (); (); (); (); (); (); (); (). Number indicates clone from PCR. and sequences from genomic database (e.g. Ag-Jock-1, AaJockeyEle2) can be found in the TEfam database [57]. See additional files and for alignments used for phylogenetic inference

The non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity-2

<p><b>Copyright information:</b></p><p>Taken from "The non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity"</p><p>http://www.biomedcentral.com/1471-2148/7/112</p><p>BMC Evolutionary Biology 2007;7():112-112.</p><p>Published online 9 Jul 2007</p><p>PMCID:PMC1947958.</p><p></p>ase (RT) domain. Arrows indicate the 939 bp region amplified by PCR that was used for phylogenetic inference. A canonical polyadenylation signal sequence is present in the 3' end of (not shown) Regions used for copy number determination by database search in Table 1 are shown by horizontal lines

Pure early zygotic genes in the Asian malaria mosquito Anopheles stephensi

Abstract Background The Asian malaria mosquito, Anopheles stephensi, is a major urban malaria vector in the Middle East and on the Indian subcontinent. Early zygotic transcription, which marks the maternal-to-zygotic transition, has not been systematically studied in An. stephensi or any other Anopheles mosquitoes. Improved understanding of early embryonic gene expression in An. stephensi will facilitate genetic and evolutionary studies and help with the development of novel control strategies for this important disease vector. Results We obtained RNA-seq data in biological triplicates from four early An. stephensi embryonic time points. Using these data, we identified 70 and 153 pure early zygotic genes (pEZGs) under stringent and relaxed conditions, respectively. We show that these pEZGs are enriched in functional groups related to DNA-binding transcription regulators, cell cycle modulators, proteases, transport, and cellular metabolism. On average these pEZGs are shorter and have less introns than other An. stephensi genes. Some of the pEZGs may arise de novo while others have clear non-pEZG paralogs. There is no or very limited overlap between An. stephensi pEZGs and Drosophila melanogaster or Aedes aegypti pEZGs. Interestingly, the upstream region of An. stephensi pEZGs lack significant enrichment of a previously reported TAGteam/VBRGGTA motif found in the regulatory region of pEZGs in D. melanogaster and Ae. aegypti. However, a GT-rich motif was found in An. stephensi pEZGs instead. Conclusions We have identified a number of pEZGs whose predicted functions and structures are consistent with their collective roles in the degradation of maternally deposited components, activation of the zygotic genome, cell division, and metabolism. The pEZGs appear to rapidly turn over within the Dipteran order and even within the Culicidae family. These pEZGs, and the shared regulatory motif, could provide the promoter or regulatory sequences to drive gene expression in the syncytial or early cellular blastoderm, a period when the developing embryo is accessible to genetic manipulation. In addition, these molecular resources may be used to achieve sex separation of mosquitoes for sterile insect technique

RT-PCR validation of transcriptome data.

<p>A) AAEL008851, an example of an EZG gene where both RT-PCR and transcriptome sequencing show expression at the 2–3 hr time range. B) AAEL001543, a zygotic gene with a similar profile as AAEL008851 but which has less expression in the 2–4 hr time range (note very faint band from RT-PCR at 2–3 hr was present that may not be discernable in image). C) AAEL008722, a zygotic gene having expression detected later at 4–5 hr by PCR. Normalized expression values of each transcript from the transcriptome data are at the bottom of each figure. Note that AAEL008722 is not included in our “EZG set” as it is not present until the 4–8 hr time range in the transcriptome data.</p