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Swamp eel assembly and gene annotation

Assembly

The M_albus_1.0 assembly was submitted by Wuhan University on January 2017. The assembly is on scaffold level, consisting of 71,879 contigs assembled into 20,622 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 22,239 while the scaffold N50 is 2,106,322.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001952655.1

Gene annotation

The Asian swamp eel, swamp eel, rice eel, or white ricefield eel (Monopterus albus) is a commercially important, air-breathing species of fish in the Synbranchidae family. Originating in the waters of East and Southeast Asia, it has been identified as an invasive species in the North American Everglades.

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

AssemblyM_albus_1.0, INSDC Assembly GCA_001952655.1, Jan 2017
Base Pairs684,144,148
Golden Path Length684,144,148
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes22,145
Non coding genes527
Small non coding genes505
Long non coding genes2
Misc non coding genes20
Pseudogenes36
Gene transcripts33,565

Other

Genscan gene predictions33,206

About this species