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Guppy assembly and gene annotation

Assembly

The Guppy_female_1.0+MT assembly was submitted by Max Planck Institute for Developmental Biology on May 2014. The assembly is on chromosome level, consisting of 40,144 contigs assembled into 3,029 scaffolds. From these sequences, 23 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 41,908 while the scaffold N50 is 5,270,359.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000633615.2

Gene annotation

The guppy (Poecilia reticulata), also known as millionfish and rainbow fish, is one of the world's most widely distributed tropical fish, and one of the most popular freshwater aquarium fish species. It is a member of the family Poeciliidae and, like almost all American members of the family, is live-bearing. Guppies, whose natural range is in northeast South America, were introduced to many habitats and are now found all over the world. They are highly adaptable and thrive in many different environmental and ecological conditions. Male guppies, which are smaller than females, have ornamental caudal and dorsal fins. Wild guppies generally feed on a variety of food sources, including benthic algae and aquatic insect larvae. Guppies are used as a model organism in the fields of ecology, evolution, and behavioural studies.

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

AssemblyGuppy_female_1.0_MT, INSDC Assembly GCA_000633615.2, Apr 2014
Base Pairs731,622,281
Golden Path Length731,622,281
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes22,871
Non coding genes358
Small non coding genes338
Long non coding genes2
Misc non coding genes18
Pseudogenes25
Gene transcripts34,730

Other

Genscan gene predictions39,344

About this species