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Overview

StatusReference proteome
Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 21,752
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000008549
Taxonomy6238 - Caenorhabditis briggsae
StrainAF16
Last modifiedJanuary 15, 2020
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000004555.3 from ENA/EMBL full
BuscoC:98.4%[S:97.8%,D:0.6%],F:1.4%,M:0.2%,n:982
CompletenessStandard

Caenorhabditis briggsae is a nematode roundworm that is almost indistinguishable from the model-organism nematode Caenorhabditis elegans. It also shares many other features such as chromosome number, habitat and behavior which make it an ideal candidate for comparative genomics studies, especially as 93% of the predicted protein-coding genes have clear C. elegans orthologs.

Like C. elegans the C. briggsae embryo goes through four larval stages before becoming a mature adult. In response to over-crowding or an inadequate food supply the worm can adopt a dauer larval stage. In this stage the worm can survive for up to three months. Most worms are found in this stage. Sexual reproduction occurs by an adult hermaphrodite self-fertilizing.

The reference proteome for C. briggsae (strain AF16) is derived from a hybrid sequencing approach combining whole-genome assembly with whole-genome shotgun sequencing (WGS). The C. briggsae genome size is approximately 104 Mb, slightly larger than that of the C. elegans. The difference is mainly due to the larger non-genic repetitive DNA content in C. briggsae's genome. The number of protein-coding genes is estimated to be 19,507.

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Chromosome I3071
Chromosome II3318
Chromosome III2885
Chromosome IV3260
Chromosome V4763
Chromosome X3747
Unassembled WGS sequence1267
Mitochondrion7
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Main funding by: National Institutes of Health

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