Anopheles coluzzii (Ngousso) (AcolN1)

Anopheles coluzzii (Ngousso) Assembly and Gene Annotation

The Anopheles coluzzii data and its display on Ensembl Genomes are made possible through a joint effort by the Ensembl Genomes group and VectorBase, a component of VEuPathDB.

About Anopheles coluzzii

Anopheles coluzzii, formerly known as Anopheles gambiae M molecular form, was defined as a separate species in 2013 (Coetzee et al.). An. coluzzii belongs to the Anopheles gambiae species complex, which consists of at least seven species.

Maureen Coetzee, Richard H. Hunt, Richard Wilkerson, Alessandra Della Torre, Mamadou B. Coulibaly & Nora J. Besansky. 2013. Anopheles coluzzii and Anopheles amharicus, new members of the Anopheles gambiaecomplex. Zootaxa 3619 (3): 246--274.

Ngousso strain

The Ngousso colony was created in 2006 from the broods of approximately 100 wild-caught pure An. coluzzii females in Cameroon (
"A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing
"
, Kingan et al, Genes 2019, 10, 62; doi:10.3390/genes10010062 ). The colony is partially inbred, and has been used extensively in experimental infection studies.

Source: VectorBase

AcolN1 assembly

AcolN1 is a high-quality de novo genome assembly from a single Anopheles coluzzii mosquito from the Ngousso colony, as decribed in the paper 'A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing', Kingan et al, Genes (Basel). 2019 Jan; 10(1): 62. The assembly was generated using a modified SMRTbell library construction protocol, and consists of a primary de novo assembly of 372 contigs totaling 266 Mb in length, 665 alternate haplotigs, and with half of the assembly in contigs (contig N50) of 3.5 Mb or longer. The additional phased haplotype sequences spanned a total of 78.5 Mb (i.e., 29% of the total genome size was separated into haplotypes), with a contig N50 of 223 kb. A 4.24 Mb bacterial genome, closely related to Elizabethkingia anophelis, was also identified and removed from the assembly. Two full length copies of the mitochondrial chromosome were isolated, differeing by only a single base. One of mtDNA copies was discarded from the final assembly, and the other retained with the sequence accession CM014284.1.

The new PacBio assembly is highly concordant with the AgamP4 PEST reference over the entire genome, allowing the placement of the long PacBio contigs into chromosomal contexts. In addition, the high contiguity of the PacBio contigs allows for the resolution of many gaps in the Anopheles gambiaechromosomal PEST strain 'contigs'.

AcolN1.1 gene set

Community annotation patch build for July 2019.

References

  1. A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing.
    Kingan SB, Heaton H, Cudini J, Lambert CC, Baybayan P, Galvin BD, Durbin R, Korlach J, Lawniczak MKN. . 2019. Genes (Basel). 10(1)

Picture credit: VectorBase.org

Statistics

Summary

AssemblyAcolN1, INSDC Assembly GCA_004136515.2,
Database version106.1
Golden Path Length251,414,185
Genebuild byVEuPathDB
Genebuild methodImport build
Data sourcePacific Biosciences

Gene counts

Coding genes12,773
Non coding genes469
Small non coding genes467
Long non coding genes2
Gene transcripts15,163

About this species