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Table 5 Comparison of published genotypes and associated phenotypes with GVs detected in this study

From: Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Genes impacted

Published data

Our genomic analysis

Genotype (GVs)

Phenotype (Trait)

Reference

Result in our dataset

Coordinates

Observations

npr-1

SNV;G > T;V215F

Intake of CO2/O2; Social behavior and food response; Pathogen susceptibilty

[29, 36, 38]

Found

X:4768758

N.A.

glb-5

Deleted 5th exon

Intake of CO2/O2

[29, 30]

Found after inspection

V:5562441..5562810

NAHR-based deletion

plg-1 (no gene model associated)

Deletion of LTR-Retrotransposon (retr-1; F44E2.2)

Copulatory plug formation

[28]

Found after inspection

III:8852505..8861364

Repeat at boundary

C49G7.1, D1065.3

2.9 kbp deletion

N.R.

[48]

Found

V:4057628..4060567

N.A.

gst-38

Multiple SNVs

N.R.

[48, 50]

Found

V:15915782, 15915630, 15915570, 15915519, 15915351, 15915441, 15915316, 15915620, 15915480, 15915498, 15915561, 15915489, 15915347, 15915780, 15915777, 15915687, 15915318, 15915672, 15915666, 15915284, 15915393, 15915624, 15915837, 15915879, 15915417, 15915387, 15915439

N.A.

tra-3

SNV;T > C;F96L

Temperature-size rule

[32]

Found

IV:14442336

N.A.

ppw-1

SNV;T > C;F35S

Germline RNAi

[33]

Found

I:4186589

N.A.

Insertion;ATT

Found after inspection

I:4186704..4186705

N.A.

SNV;A > G;T245A

Found

I:4187463

N.A.

Deletion;C

Found

I:4187632

N.A.

SNV;C > T;L474L

Found

I:4188304

N.A.

SNV;A > G;D691G

Found

I:4189045

N.A.

SNV;A > G;K777E

Found after inspection

I:4189302

Falls in non-unique region

tyra-3

184 bps deletion

Patch-leaving

[81]

Found

X:4948657..4948841

Non-coding region

zeel-1

High divergence, 19 kb deletion

Required for compatibility between N2 and CB4856

[26]

Not found

N.A.

Divergent, complex region

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BMC Genomics

ISSN: 1471-2164

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