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Eastern happy assembly and gene annotation

Assembly

The fAstCal1.2 assembly was submitted by SC on June 2018. The assembly is on chromosome level, consisting of 739 contigs assembled into 249 scaffolds. From these sequences, 22 chromosomes have been built. 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 4,438,245 while the scaffold N50 is 38,669,361.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_900246225.3

Gene annotation

Astatotilapia is a genus of fish in the family Cichlidae found in Eastern and Northern Africa, and Western Asia. Many species have been moved between this genus and Haplochromis, and while some consensus has been reached in recent years, their mutual delimitation is still far from settled. Based on mtDNA, Astatotilapia as currently defined is polyphyletic.

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

AssemblyfAstCal1.2, INSDC Assembly GCA_900246225.3, May 2018
Base Pairs880,428,986
Golden Path Length880,428,986
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJun 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.12

Gene counts

Coding genes27,018
Non coding genes939
Small non coding genes893
Long non coding genes3
Misc non coding genes43
Pseudogenes44
Gene transcripts42,580

Other

Genscan gene predictions40,839

About this species