Comment

. 2017 Jun 14;18(1):112.

doi: 10.1186/s13059-017-1231-1.

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

Susanne Bornelöv^{1

2}, Eyal Seroussi³, Sara Yosefi³, Ken Pendavis⁴, Shane C Burgess⁴, Manfred Grabherr^{1

5}, Miriam Friedman-Einat⁶, Leif Andersson^{7

8

9}

Affiliations

¹ Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden.
² Present Address: Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
³ Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.
⁴ College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA.
⁵ Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden.
⁶ Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel. miri.einat@mail.huji.ac.il.
⁷ Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden. leif.andersson@imbim.uu.se.
⁸ Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden. leif.andersson@imbim.uu.se.
⁹ Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA. leif.andersson@imbim.uu.se.

PMID: 28615067
PMCID: PMC5470226
DOI: 10.1186/s13059-017-1231-1

Comment

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

Susanne Bornelöv et al. Genome Biol. 2017.

. 2017 Jun 14;18(1):112.

doi: 10.1186/s13059-017-1231-1.

Authors

Susanne Bornelöv^{1

2}, Eyal Seroussi³, Sara Yosefi³, Ken Pendavis⁴, Shane C Burgess⁴, Manfred Grabherr^{1

5}, Miriam Friedman-Einat⁶, Leif Andersson^{7

8

9}

Affiliations

¹ Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden.
² Present Address: Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
³ Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.
⁴ College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA.
⁵ Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden.
⁶ Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel. miri.einat@mail.huji.ac.il.
⁷ Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden. leif.andersson@imbim.uu.se.
⁸ Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden. leif.andersson@imbim.uu.se.
⁹ Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA. leif.andersson@imbim.uu.se.

PMID: 28615067
PMCID: PMC5470226
DOI: 10.1186/s13059-017-1231-1

Abstract

Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases. Hence, the occurrence of syntenic groups of vertebrate genes that have not been observed in Aves does not prove the evolutionary loss of such genes.Please see related Research article: http://dx.doi.org/10.1186/s13059-014-0565-1 and Please see response from Lovell et al: https://www.dx.doi.org/10.1186/s13059-017-1234-y.

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References

1. Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, et al. Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol. 2014;15:565. doi: 10.1186/s13059-014-0565-1. - DOI - PMC - PubMed
1. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014;346:1311–20. doi: 10.1126/science.1251385. - DOI - PMC - PubMed
1. Seroussi E, Cinnamon Y, Yosefi S, Genin O, Smith JG, Rafati N, et al. Identification of the long-sought leptin in chicken and duck: expression pattern of the highly GC-rich avian leptin Fits an autocrine/paracrine rather than endocrine function. Endocrinology. 2016;157:737–51. doi: 10.1210/en.2015-1634. - DOI - PubMed
1. Hron T, Pajer P, Paces J, Bartunek P, Elleder D. Hidden genes in birds. Genome Biol. 2015;16:164. doi: 10.1186/s13059-015-0724-z. - DOI - PMC - PubMed
1. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52. doi: 10.1038/nbt.1883. - DOI - PMC - PubMed

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

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