Ensembl mobile site help

Things to know when navigating the Ensembl mobile site

Search box

Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more.

Top navigation

Touch MENU button to open the main menu and touch again to close.

Touch MENU

Left hand side menu

Touch the left menu icon () or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close.

The ? icon

Touch the icon to get help

And don't forget to send us your comments using the feedback link inside the main menu.

EnsemblEnsembl Home

Lyretail cichlid assembly and gene annotation

Assembly

The NeoBri1.0 assembly was submitted by Broad Institute on December 2011. The assembly is on scaffold level, consisting of 118,197 contigs assembled into 9,099 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 13,047 while the scaffold N50 is 4,430,025.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000239395.1

Gene annotation

Neolamprologus brichardi is a species of cichlid endemic to the alkaline waters of Lake Tanganyika in East Africa. It is a popular aquarium fish kept in the fishkeeping hobby, where it is known under a variety of common names including Princess cichlid, Princess of Burundi, Lyretail cichlid, Fairy cichlid and Brichard's lamprologus. In addition, the species is also the subject of numerous studies on fish behaviour. It is closely related to N. pulcher from the southern half of Lake Tanganyika (N. brichardi is more widespread) and some have recommended merging the two into a single species.N. brichardi is notable in a number of ways. This fish is a substrate spawner (lays eggs on substrate), utilizing the rocky rubble to do so. It is one of the few substrate-spawning cichlid that also schools. It is not unheard of to find a school numbering near 100,000 individuals within a 50 m square area. It is one of the few fish in Africa that utilizes a collective nursery. This means that adults, sub-adults, and even half-grown fry all participate in a multi-generational rearing of the fry. N. brichardi individuals not only care for their own fry but also the fry of those around them, all while keeping vigil over other adults still actively spawning. This is similar to the cooperative breeding system of a related species of cichlid, N. pulcher, in that N. pulcher individuals will care for the offspring of others.N. brichardi specializes on feeding from the rocky biocover, picking at small crustaceans and invertebrates. It will also feed on swarms of plankton when available.

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyNeoBri1.0, INSDC Assembly GCA_000239395.1, Dec 2011
Base Pairs847,910,432
Golden Path Length847,910,432
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,596
Non coding genes776
Small non coding genes759
Long non coding genes3
Misc non coding genes14
Pseudogenes39
Gene transcripts32,961

Other

Genscan gene predictions36,842

About this species