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Table 3 Copy number variants of turkey plus broiler and layer chickens compared to Red Jungle Fowl. Numbers represent fold-changes compared to Red Jungle Fowl (when significantly different). Table also notes whether the CNV is associated with a gene/genes and degree of conservation.

From: Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

CNV

Chromosome Location

Length

Fold change of CNV cf, Red Jungle Fowl

CNV Hotspot?

Genes/ESTs

Conserved in Mammals?

Conserved in Xenopus/Zebrafish?

Comments

  

(kb)

Broiler

Layer

Turkey

     

1

chr1:86445000–86475000

30,000

  

-5.65

 

yes

no

yes

novel proteins, birds/fish/frogs, Phospholipase A2, a family of secretory and cytosolic enzymes

2

chr1:104475000–104505000

30,000

-1.95

   

yes

yes

yes

novel protein, birds/fish/frogs

3

chr1:140595000–140625000

30,000

2.26

 

-5.52

yes

yes

yes

yes

similar to RAN binding protein 2

4

chr1:144225000–144255000

30,000

  

-3.54

 

yes

yes

yes

novel proteins/RNAs

5

chr1:165885000–165975000

90,000

-2.59

-2.24

  

yes

yes

yes

interleukin enhancer binding factor 3

6

chr1:197715000–197745000

30,000

  

-2.83

 

yes

no

yes

novel, birds/frogs, similar to Gab2, lipid binding motifs

7

chr10:30000–150000

120,000

  

-1.82

 

yes

yes

yes

olfactory receptors

8

chr13:510000–570000

60,000

-2.05

   

yes

yes

yes

protocadherin cluster

9

chr13:18885000–18903772

18,772

  

-4.73

 

yes

yes

yes

novel proteins/RNAs

10

chr16:15000–426425

411,425

-1.48

-2.68

-4.73

yes

yes

yes

yes

MHC

11

chr2:25725000–25785000

60,000

 

-1.57

  

no

yes

yes

conserved non-coding region

12

chr2:49185000–49215000

30,000

 

2.13

  

yes

no

yes

novel, birds/frogs, T cell receptor, gamma cluster

13

chr2:53925000–54225000

300,000

  

-1.62

 

yes

yes

yes

Thiamin pyrophosphokinase 1

14

chr27:30000–930000

900,000

  

-1.81

 

yes

yes

yes

gamma filamin protein, mainly due to cluster of feather keratins

15

chr27:165000–255000

90,000

 

-1.47

  

yes

no

yes

novel proteins/RNAs birds/fish

16

chr3:113550000–113646334

96,334

2.34

2.30

-2.59

yes

yes

yes

yes

39S ribosomal protein L19, GC-rich sequence DNA-binding factor TCF9-like, novel proteins/RNAs

17

chr4:88935000–89025000

90,000

 

-2.20

-2.42

yes

yes

no

no

CD8alpha

18

chr6:4695000–4785000

90,000

-1.70

 

-3.98

 

yes

yes

yes

Pro-neuregulin-3

19

chr6:11475000–11505000

30,000

  

-9.91

 

yes

no

no

novel proteins/RNAs

20

chr7:23625000–23925000

300,000

  

1.67

 

yes

yes

yes

many genes, mainly due to TUBA-cluster

21

chrE64:22523–22523

n/d

  

-1.41

 

yes

yes

yes

Zinc finger cluster

22

chrZ:71535000–71745000

210,000

3.45

3.38

-7.01

yes

yes

yes

yes

male/female difference, similar to rac GTPase activating protein

Total number of CNV loci cf. Red Jungle Fowl

8

8

16

6