Southern tamandua (Tamandua tetradactyla)
The southern anteater is the most abundant anteater species in the Neotropics. Read more about southern tamanduas on National Geographic website.
Tamandua by Molly Lockhart, [CC BY 2.0], via flickr.com
Chromosome-length genome assembly
Download the Tamandua_tetradactyla_M3075_MaSuRCA_1_07_2020_final_genome_scf_HiC.fasta.gz file containing the chromosome-length (2n=56) assembly of the southern tamandua genome. All modifications with respect to the draft (see below) are annotated in the Tamandua_tetradactyla_M3075_MaSuRCA_1_07_2020_final_genome_scf_HiC.assembly file. Some basic stats associated with the new reference, Tamandua_tetradactyla_M3075_MaSuRCA_1_07_2020_final_genome_scf_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
3,318,038,110 | 8,920 | 2,227,613 | 11,508,960 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
3,319,533,610 | 5,841 | 124,746,971 | 238,072,295 |
Draft
The chromosome-length genome assembly is based on the draft assembly Tamandua_tetradactyla_M3075_MaSuRCA_1_07_2020_final_genome_scf, credited below.
The assembly shared here is a Hi-C upgrade to a draft genome hybrid assembly generated by combining Nanopore long reads with Illumina short reads by Rémi Allio, Frédéric Delsuc and team at Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier as part of the ConvergeAnt Project. The original sample used for the initial draft assembly comes from a fresh roadkill individual found near Kourou (French Guiana) in 2018. The corresponding specimen (M3075) is part of the JAGUARS collection curated by Benoit de Thoisy (Institut Pasteur de Cayenne and Kwata NGO, French Guiana). The sample used for Hi-C came from the Houston Zoo.
Method
3D Assembly was performed using 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome was reviewed using Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018). See Methods for more information.
Hi-C sample
The blood sample for in situ Hi-C preparation was donated by a female individual named Fiera, and provided to us by Houston Zoo. We thank SeaWorld, San Antonio Zoo and Moody Gardens for additional southern tamandua samples.
Hi-C Contact maps
Hi-C data was aligned to the draft reference using Juicer (Durand, Shamim et al., Cell Systems, 2016), and contact maps visualizing the alignments with respect to the draft and the new reference were built using 3D-DNA (Dudchenko et al., Science, 2017). The contact maps can be explored below via Juicebox.js interactive tool (Robinson et al., Cell Systems, 2018). (Please note that the interactive figures are scaled 1:2.) To explore the assembly in greater detail, please download the .hic and .assembly files from the data release folder and use Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018).
References
If you use this genome assembly in your research, please check that the conditions of use associated with the draft permit it, and acknowledge the following work.
The assembly shared here is a Hi-C upgrade to a draft genome hybrid assembly generated by combining Nanopore long reads with Illumina short reads by Rémi Allio, Frédéric Delsuc and team at Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier as part of the ConvergeAnt Project. The original sample used for the initial draft assembly comes from a fresh roadkill individual found near Kourou (French Guiana) in 2018. The corresponding specimen (M3075) is part of the JAGUARS collection curated by Benoit de Thoisy (Institut Pasteur de Cayenne and Kwata NGO, French Guiana). The sample used for Hi-C came from the Houston Zoo.
Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.
Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.
Disclaimer
This is a work in progress. If you notice any discrepancies in the map or have data that confirms or contradicts the suggested reference, please email us at thednazoo@gmail.com or leave a comment on the Forum.