1. Качество сборки генома Takifugu rubripes

Название вида Takifugu rubripes (torafugu/бурый фугу)
Число сборок 1
Общая длина 391,484,725
Число контигов 30,861
Число скаффолдов 7,091
N50 (contig/scaffold) 52,883/928,938
L50 (contig/scaffold) 1,722/113
Число аннотированных белков 21,323
Публикация в PubMed Ссылка на контиг

Таблица 1. Описание сборки GCF_000180615.1 генома Takifugu rubripes

2. Feature Keys

Ключ Описание Пример
gene region of biological interest identified as a gene and for which a name has been assigned. 
complement(967..3657)
/gene="cd79b"
/note="Derived by automated computational analysis using
gene prediction method: Gnomon."
/db_xref="GeneID:101064965"
CDS coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon); feature includes amino acid conceptual translation. 
join(58432..58562,58761..58867,59489..59712)
/gene="mrpl43"
/note="Derived by automated computational analysis using
gene prediction method: Gnomon."
/codon_start=1
/product="39S ribosomal protein L43, mitochondrial"
/protein_id="XP_003961070.1"
/db_xref="GeneID:101065870"
/translation="MGSRAGPSRFLQSVLHNGIGRYVCQLKRISIIFSKNAQSSLGVR
EFIENGAIDYANKNPSTVVYVAPQACRIPKIVAEYLNGNVREETVTNKTSSQISQLLT
KLTNQSGLDIIRIRKPFHTNNPSIQGQWHPFTNRPPSIGPIRPVKIDSKTQ"
mRNA messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR). 
join(7..66,146..232,321..470,647..727,806..926)
/gene="LOC101064747"
/product="interferon alpha-2-like"
/note="Derived by automated computational analysis using
gene prediction method: Gnomon. Supporting evidence
includes similarity to: 15 Proteins, and 84% coverage of
the annotated genomic feature by RNAseq alignments"
/transcript_id="XM_003961016.2"
/db_xref="GeneID:101064747"
assembly_gap gap between two components of a genome or transcriptome assembly. 
43702..43796
/estimated_length=95
/gap_type="within scaffold"
/linkage_evidence="unspecified"
misc_RNA any transcript or RNA product that cannot be defined by other RNA keys (prim_transcript, precursor_RNA, mRNA, 5'UTR, 3'UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron, polyA_site, ncRNA, rRNA and tRNA). 
join(21284..21358,21463..21597,21760..21921,22002..22181,
22264..22398,22490..22838)
/gene="LOC105416246"
/product="reticulon-1-like, transcript variant X5"
/note="Derived by automated computational analysis using
gene prediction method: Gnomon. Supporting evidence
includes similarity to: 100% coverage of the annotated
genomic feature by RNAseq alignments, including 1 sample
with support for all annotated introns"
/transcript_id="XR_964582.1"
/db_xref="GeneID:105416246"
ncRNA a non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNA transcript 
complement(join(260865..261418,262215..262390))
/ncRNA_class="lncRNA"
/gene="LOC105416261"
/product="uncharacterized LOC105416261"
/note="Derived by automated computational analysis using
gene prediction method: Gnomon. Supporting evidence
includes similarity to: 100% coverage of the annotated
genomic feature by RNAseq alignments, including 1 sample
with support for all annotated introns"
/transcript_id="XR_964457.1"
/db_xref="GeneID:105416261"
tRNA mature transfer RNA, a small RNA molecule (75-85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence. 
317747..317817
/gene="trnag-ccc"
/product="tRNA-Gly"
/inference="COORDINATES: profile:tRNAscan-SE:1.23"
/note="transfer RNA glycine (anticodon CCC); tRNA features
were annotated by tRNAscan-SE; Derived by automated
computational analysis using gene prediction method:
tRNAscan-SE."
/anticodon=(pos:317779..317781,aa:Gly,seq:ccc)
/db_xref="GeneID:101060930"

Таблица 2. Feature keys

3. The Fugu Genome Sequencing Consortium

Проект был основан в 2000 году с целью полного секвенирования генома рыбы фугу вида Takifugu rubripes, уже через год был получен его "черновой" вариант. Последняя сборка (FUGU5) была представлена октябре 2011 года, в июне того же года вышла последняя публикация проекта. Описание сборки FUGU5 приведено в таблице 1.

The Fugu Genome Sequencing Consortium - международный проект, в котором приняли участие исследовательские институты Сингапура и США: Institute of Molecular and Cell Biology (Singapore), Joint Genome Institute (USA), Institute for Systems Biology (USA); а также Human Genome Mapping Project (UK).

4. Таблица митохондриальных генов

Для описания я выбрала японского шмеля Bombus hypocrita sapporensis как представителя таксона Arthropoda. Текст запроса в ENA:

tax_tree(1079038) AND mol_type="genomic DNA" AND topology="CIRCULAR" AND organelle="mitochondrion"

Было найдено три записи в "Release". Выбранный AC: AP017370.

Таблицу митохондриальных генов белков можно посмотреть здесь.