Nucleotide Sequencing of the HoxA Gene Cluster Using Gorilla Fosmid Clones

Overview

Journal J Genomics

Specialty Genetics

Date 2020 Sep 16

PMID 32934753

Authors

Takashi Kitano

Choong-Gon Kim

Naruya Saitou

Affiliations

Soon will be listed here.

Abstract

We sequenced the western gorilla () HoxA cluster region using seven fosmid clones, and found that the total tiling path sequence was 214,185 bp from the 5' non-genic region of HoxA1 to the 3' non-genic region of Evx1. We compared the nucleotide sequence with the gorilla genome sequence in the NCBI database, and the overall proportion of nucleotide difference was estimated to be 0.0005-0.0007. These estimates are lower than overall genomic polymorphism in gorillas.

References

Matsunami M, Sumiyama K, Saitou N . Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis. J Mol Evol. 2010; 71(5-6):427-36. DOI: 10.1007/s00239-010-9396-1. View

Scally A, Dutheil J, Hillier L, Jordan G, Goodhead I, Herrero J . Insights into hominid evolution from the gorilla genome sequence. Nature. 2012; 483(7388):169-75. PMC: 3303130. DOI: 10.1038/nature10842. View

Kim C, Fujiyama A, Saitou N . Construction of a gorilla fosmid library and its PCR screening system. Genomics. 2003; 82(5):571-4. DOI: 10.1016/s0888-7543(03)00174-5. View

Watanabe H, Fujiyama A, Hattori M, Taylor T, Toyoda A, Kuroki Y . DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 2004; 429(6990):382-8. DOI: 10.1038/nature02564. View

Nei M, Gojobori T . Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986; 3(5):418-26. DOI: 10.1093/oxfordjournals.molbev.a040410. View

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J . Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921. DOI: 10.1038/35057062. View

. Finishing the euchromatic sequence of the human genome. Nature. 2004; 431(7011):931-45. DOI: 10.1038/nature03001. View

Kumar S, Stecher G, Tamura K . MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016; 33(7):1870-4. PMC: 8210823. DOI: 10.1093/molbev/msw054. View

Ewing B, Hillier L, Wendl M, Green P . Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998; 8(3):175-85. DOI: 10.1101/gr.8.3.175. View

10.

Matsunami M, Saitou N . Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain. Genome Biol Evol. 2012; 5(1):140-50. PMC: 3595034. DOI: 10.1093/gbe/evs128. View

11.

Santini S, Boore J, Meyer A . Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res. 2003; 13(6A):1111-22. PMC: 403639. DOI: 10.1101/gr.700503. View

12.

Gordon D, Abajian C, Green P . Consed: a graphical tool for sequence finishing. Genome Res. 1998; 8(3):195-202. DOI: 10.1101/gr.8.3.195. View