Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

Table 1 Characterization of the novel genes reported missing in previous studies

Previously reported list	No. of missing genes	Found in our intermediate set	Found in our high-confidence list	Gene symbols
Predicted absent in birds [1]	274	36 (13%)	8 (3%)	*FLT3LG, LPPR2, NPHS1, PLCB3* ^a, PRSS8, *RCN3, TRMT1, TSPAN31*
Predicted missing in chickens but not in all birds [1]^b	336	152 (45%)	50 (15%)	ALKBH7, ASB16, ATAT1, ATG4D, B9D2, CACNG7, CACNG8, CAMSAP3, *CARM1, CCDC106, CCDC120, CCDC22, CIC, CLASRP, CLPP, COPZ1, CYTH2, ESYT1, GEMIN7, GPKOW, GTF2F1, JOSD2, KRI1, LMTK3, MAP2K7, METTL1, METTL3, MRPS18B, NDUFB7, PIH1D1, POU6F1, PPP1R12C, PPP1R18, PPP5C, PRKCSH, PRPF31, PRR12, SAMD1, SCAF1, SEMA4C, SLC39A7, SMG9, SSR4, TFPT, TRAPPC1, TSR2, U2AF2, UXT, YIF1B, ZNF653*
Predicted absent in birds [2]	640	100 (16%)	29 (4.5%)	*ADAT3, ALKBH7, C11ORF95, C2ORF68, CCDC22, CDIPT, CGREF1, CIC, CXXC1, FRMD8, HUWE1, IKBKG, KRI1, LMTK3, MBD1, MUS81, NPHS1, OPA3, PHF1, PIH1D1, PLCB3* ^a, PPP1R12C, PRKCSH, RCE1, SSSCA1, TFPT, *TNF* ^d, UXT, ZNF653
Predicted absent by both studies [1, 2]	99	7 (7%)	2 (2%)	*NPHS1* ^c, PLCB3 ^a
Lost adipokines [6]	4	1 (25%)	1 (25%)	*TNF* ^d

Eleven genes are shared between row 2 (Lovell et al. [1]) and row 3 (Zhang et al. [2]): ALKBH7, CCDC22, CIC, KRI1, LMTK3, PIHID1, PPP1R12C, PRKCSH, TFPT, UXT, and ZNF653
^a PLCB3 was selected manually from the intermediate list of novel genes as a dropout due to misannotation of its quail (Coturnix japonica) ortholog (LOC107307599), demonstrating that the intermediate gene list (Additional file 1: Table S4) may contain additional novel genes
^bBased on the genes listed in Tables S4a, S4b, S6a, and S6b in Lovell et al. [1]
^cAlso reported missing in other publications (e.g. [7, 14])
^dAlso reported missing also in Zhang et al. [2] and in additional publications (e.g. [10, 15])
(i) Bold and underlined, (ii) underlined, (iii) underlined by dashed line, and (iv) non-underlined symbols represent (i) novel sequences with no sequence similarity in any genome build, (ii) sequences present in Galgal5 but lacking annotation, (iii) sequences present in Galgal5 as uncharacterized or putative, or (iv) sequences present and annotated in Galgal5, respectively

ISSN: 1474-760X