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Mangrove rivulus assembly and gene annotation

Assembly

The ASM164957v1 assembly was submitted by Sungkyunkwan University on May 2016. The assembly is on scaffold level, consisting of 26,350 contigs assembled into 3,073 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 57,884 while the scaffold N50 is 2,229,659.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001649575.1

Gene annotation

The mangrove killifish or mangrove rivulus, Kryptolebias marmoratus (syn. Rivulus marmoratus), is a species of fish in the Aplocheilidae family. It lives in brackish and marine waters (less frequently in fresh water) along the coasts of Florida, through the Antilles, and along the eastern and northern Atlantic coasts of Mexico, Central America and South America (south to Brazil). It has a very wide tolerance of both salinity (0—68 ‰) and temperature (12–38 °C or 54–100 °F), can survive for about two months on land, and mostly breeds by self-fertilization. It is typically found in areas with red mangrove and sometimes lives in burrows of Cardisoma guanhumi crabs.The mangrove rivulus is up to 7.5 cm (3.0 in) long, but most individuals are 1–3.8 cm (0.4–1.5 in).Overall the mangrove rivulus is widespread and not threatened, but in the United States it is considered a Species of Concern by the National Marine Fisheries Service.

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

AssemblyASM164957v1, INSDC Assembly GCA_001649575.1, May 2016
Base Pairs680,366,784
Golden Path Length680,366,784
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes21,930
Non coding genes347
Small non coding genes332
Long non coding genes3
Misc non coding genes12
Pseudogenes37
Gene transcripts30,573

Other

Genscan gene predictions39,032

About this species