Table 2

Tentatively annotated fast evolving transcript fragments and their sequence divergence as compared to the closest ortholog in the teleost mRNA refseq database and in the Hypostomus gr. plecostomus EST dataset.

contig

mRNA refseq annotation according to closest teleost ortholog

Species

Cds/UTR

A.temminckii vs closest teleost ortholog in mRNA refseq

A. temminckii vs H. gr. plecostomus


342

zgc:175146

Dr

3'UTR

0.4411

0.2990

435

interferon regulatory factor 6 (irf6)

Dr

3'UTR

0.4824

0.3485

478

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2 (ndufaf2), nuclear gene encoding mitochondrial protein

Dr

3'UTR

0.2680

0.2531

597

similar to porcupine homolog (LOC100148644)

Dr

3'UTR

0.4824

0.3485

605

zgc:158374

Dr

cds

0.4411

0.2833

710

single-minded homolog 2 (sim2)

Dr

3'UTR

0.4411

0.3151

785

similar to pol polyprotein (LOC796496)

Dr

cds

0.3839

0.1324

809

similar to ORF1-encoded protein (LOC100004717)

Dr

5'UTR

0.4824

0.3839

1137

zgc:56382

Dr

cds

0.3485

0.2680

1451

RMD5 homolog B (rmd5b)

Ss

5'UTR

0.5042

0.1324

1479

similar to ORF1-encoded protein (LOC100004764)

Dr

3'UTR

0.2531

0.1573

1492

wu:fc33e05

Dr

3'UTR

0.3151

0.2680

1565

hypothetical LOC570897

Dr

cds

0.3316

0.2385

1614

ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) like (rac1l)

Dr

3'UTR

0.2833

0.2990

1694

similar to NLR family, pyrin domain containing 3 (LOC100002061)

Dr

3'UTR

0.3839

0.4024

1695

monoacylglycerol O-acyltransferase 2

Dr

3'UTR

0.3485

0.2531

1782

similar to G protein-coupled receptor 128 (LOC100148710)

Dr

cds

0.3839

0.2531

1819

similar to Uromodulin precursor (Tamm-Horsfall urinary glycoprotein) (THP) (LOC100007639)

Dr

cds

0.4824

0.4024

1902

hypothetical protein LOC100150258

Dr

cds

0.3839

0.1324

1905

si:dkeyp-27b10.2

Dr

cds

0.3485

0.2531

2016

zgc:64076

Dr

3'UTR

0.2680

0.1702

2029

zgc:85811

Dr

cds

0.3151

0.1833

2066

similar to CG6639 CG6639-PA (LOC100000002)

Dr

cds

0.4824

0.3151

2085

hypothetical protein LOC100149782

Dr

cds

0.2990

0.2103

2225

zgc:158374

Dr

cds

0.4614

0.4214

2342

similar to zymogen granule membrane glycoprotein 2 (LOC100005977)

Dr

cds

0.4614

0.4411

Reference fast evolving sequences

A. brevipinnis vs Danio rerio

A. brevipinnis vs H. boulengeri

cytochrome oxidase subunit I (COI)

cds

0.239

0.145

A. cirrhosus vs Danio rerio

A. cirrhosus vs H. boulengeri

reticulon 4 (RTN4) introns 1 & 2

introns

0.748

0.170


Sequence divergence was calculated using the alignment region with sequence in all species compared. Divergences were corrected using the K2P model with 2 transitions per transversion. The lowest part of the table presents the sequence divergence of two published fast evolving markers used for characterizing species or genera. Dr: Danio rerio; Ss:

Salmo salar; A.: Ancistrus; H.:Hypostomus.

Montoya-Burgos et al. BMC Genomics 2010 11:126   doi:10.1186/1471-2164-11-126

Open Data