The Genome of Anopheles darlingi , the main neotropical malaria vector

Abstract

Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector–human and vector–parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi.

Evolutionary Dynamics of Abundant Stop Codon Readthrough

“…The alignment building process is described in detail in (Neafsey et al 2015). The set of assemblies includes A. gambiae PEST (Holt et al 2002), A. gambiae Pimperena S form and A. coluzzii (formerly A. gambiae M form) (Lawniczak et al 2010), the species sequenced as part of the Anopheles 16 Genomes Project (Neafsey et al 2013), A. darlingi (Marinotti et al 2013), and the Indian strain A. stephensi (Jiang et al 2014). In summary: Multiple whole genome alignments of 21 available Anopheles assemblies were built using the MULTIZ feature of the Threaded-Blockset Aligner suite of tools (Blanchette et al 2004), employing a similar approach to that used for other multi-species whole genome alignments such as those for 12 Drosophila (Stark et al 2007) and 29 mammal (Lindblad-Toh et al 2011) genomes.…”

Estimation of Nuclear Genome Size of Three Species of Camponotus (Mayr, 1861) (Hymenoptera: Formicidae: Formicinae) and Their Cytogenetic Relationship

“…The DNA content of the ant Solenopsis invicta also showed discrepancies probably due to the methodology employed, differences in the examined cell type, or other genetic differences between the studied populations (Wurm et al, 2010). The genome size of the main Neotropical malaria vector Anopheles darlingi obtained by FCM was similar in comparison with the value obtained by sequencing the genome after estimation and addition of repetitive portions as centromeres, telomeres and other portions of the genome rich in repetitive DNA sequences (Marinotti et al, 2013). The methodology employed to estimate the genome size of C. floridanus was FIAD, which may have underestimated the value (Ardila-Garcia et al, 2010).…”

GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates

“…The CNSs that are common to the order Diptera (the CNSs that are shared between drosophids and mosquitoes) showed a pattern of being GC poor. Even when we considered species pairs with roughly the same divergence time between drosophids and mosquitoes, namely, D. melanogaster – D. ananassae (44.2 mya; Saisawang and Ketterman 2014) and Culex quinquefasciatus – Aedes aegypti (43.3 mya; Marinotti et al. 2013) the pattern of GC remained the same where drosophid CNSs were GC rich and mosquito CNSs were GC poor.…”