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Zig-zag eel assembly and gene annotation

Assembly

The fMasArm1.1 assembly was submitted by SC on May 2018. The assembly is on scaffold level, consisting of 359 contigs assembled into 126 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 8,014,513 while the scaffold N50 is 24,807,201.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_900324485.1

Gene annotation

The tire track eel (Mastacembelus armatus) is a species of ray-finned, spiny eels belonging to the genus Mastacembelus (Scopoli, 1777) of the family Mastacembelidae, and is native to the riverine fauna of India, Pakistan, Sri Lanka, Thailand, Viet Nam, Indonesia and other parts of South East Asia. The species was named Mastacembelus armatus by Lacepède in 1800. Other common names for this popular aquarium species are zigzag eel, spiny eel, leopard spiny eel and white-spotted spiny eel. This species is not only a popular aquarium fish but also as a food fish in its country of origin.

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

AssemblyfMasArm1.1, INSDC Assembly GCA_900324485.1, Mar 2018
Base Pairs593,065,986
Golden Path Length593,065,986
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.11

Gene counts

Coding genes23,333
Non coding genes888
Small non coding genes870
Long non coding genes2
Misc non coding genes16
Pseudogenes36
Gene transcripts37,087

Other

Genscan gene predictions29,427

About this species