Biodiversity Genomes
We present partial genome sequences of 50 salamander species (Urodela) from 10 genera and 4 families. These span nearly the entire range of genome sizes in salamanders, from ~14–130GB, the latter of which is among the largest of all animal genomes. Only three salamander genomes were available to this point, from Ambystomatidae (one species) and Salamandridae (two species from two genera), to which we have added Amphiumidae (one species), Plethodontidae (45 species from 6 genera), Proteidae (one species), and Sirenidae (three species from two genera). These span ~140 million years of evolutionary divergence, leaving only Cryptobranchidae, Hynobiidae, and Rhyacotritonidae as salamander families without genome assemblies. These data should facilitate additional future work on speciation and genome evolution, both within Urodela and across Animalia.
Methods
Tissues from single, wild-collected individuals were used for this study. Specimens were collected with relevant ethical approvals and state permits, and physical specimen vouchers were accessioned in registered natural history collections at accredited museums (Buckner et al. 2021). Notably, these include the holotypes of Desmognathus anicetus Pyron and Beamer 2023 and D. valtos Pyron and Beamer 2022a, and paratypes of D. adatsihi Pyron and Beamer 2022c; D. bairdi Pyron and Beamer 2023; D. balsameus Pyron and Beamer 2022c; D. campi Pyron and Beamer 2023; D. catahoula Pyron and Beamer 2023; D. cheaha Pyron et al. 2023; D. kanawha Pyron and Beamer 2022b; D. lycos Pyron and Beamer 2023; D. mavrokoilius Pyron and Beamer 2022b; D. pascagoula Pyron et al. 2022; and D. tilleyi Pyron and Beamer 2023.
DNA extraction was performed using the Qiagen DNEasy genomic extraction kit using the standard process. Paired-end sequencing libraries were constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150bp format. The resulting fastq files were trimmed of adapter/primer sequences and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v3.15.4 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Results and Data Availability
All raw read data and assembled genomes are available on Genbank:
| Amphiuma means | JAWWEG000000000 | GSU 27311 |
| Aneides aeneus | JAWWEJ000000000 | AMNH A-194066 |
| Desmognathus abditus | JASCRC000000000 | BMNH 2021.7562 |
| Desmognathus adatsihi | JAUEJF000000000 | NCSM 108356 (paratype) |
| Desmognathus aeneus | JASCRE000000000 | BMNH 2021.7563 |
| Desmognathus amphileucus | JAUCMQ000000000 | MNHN-RA 2021.0156 |
| Desmognathus anicetus | JAVSBX000000000 | USNM 596929 (holotype) |
| Desmognathus apalachicolae | JASBQJ000000000 | MNHN-RA 2021.0145 |
| Desmognathus aureatus | JAUEJG000000000 | MNHN-RA 2021.0144 |
| Desmognathus auriculatus | JASBQM000000000 | MNHN-RA 2021.0155 |
| Desmognathus bairdi | JAVKLH000000000 | MNHN-RA 2021.0132 (paratype) |
| Desmognathus balsameus | JAUBNR000000000 | BMNH 2021.7526 (paratype) |
| Desmognathus campi | JAVSBW000000000 | MNHN-RA 2021.0154 (paratype) |
| Desmognathus carolinensis | JASAFM000000000 | MNHN-RA 2021.0126 |
| Desmognathus catahoula | JAVHNH000000000 | LSUMZ 129465 (paratype) |
| Desmognathus cheaha | JAUBNS000000000 | AUM 45531 (paratype) |
| Desmognathus conanti | JASCRB000000000 | BMNH 2021.7572 |
| Desmognathus fuscus | JAUCNN000000000 | AMNH A-194084 |
| Desmognathus gvnigeusgwotli | JAUBNT000000000 | NCSM 108359 |
| Desmognathus intermedius | JAUEJH000000000 | BMNH 2021.7548 |
| Desmognathus kanawha | JAUBNU000000000 | AMNH A-193878 (paratype) |
| Desmognathus lycos | JAWWMH000000000 | NCSM 109134 (paratype) |
| Desmognathus marmoratus | JASANK000000000 | MNHN-RA 2021.0120 |
| Desmognathus mavrokoilius | JAUBNV000000000 | AMNH A-193883 (paratype) |
| Desmognathus monticola | JASANL000000000 | GMNH 52968 |
| Desmognathus ocoee | JASBQK000000000 | BMNH 2021.7529 |
| Desmognathus orestes | JASBQG000000000 | BMNH 2021.7532 |
| Desmognathus organi | JASDQV000000000 | MNHN-RA 2021.0124 |
| Desmognathus pascagoula | JASBQL000000000 | MMNS 19997 (paratype) |
| Desmognathus perlapsus | JAUEJI000000000 | MNHN-RA 2021.0118 |
| Desmognathus santeetlah | JASANM000000000 | MNHN-RA 2021.0130 |
| Desmognathus tilleyi | JAWLIA000000000 | NCSM 109130 (paratype) |
| Desmognathus valentinei | JASBQI000000000 | MMNS 19990 |
| Desmognathus valtos | JAUBNW000000000 | MNHN-RA 2021.0131 (holotype) |
| Desmognathus welteri | JASCRD000000000 | MNHN-RA 2021.0139 |
| Desmognathus wrighti | JASBQO000000000 | BMNH 2021.7561 |
| Eurycea bislineata | JBCATW000000000 | AMNH A-194067 |
| Eurycea cirrigera | JAWWEH000000000 | GSU 27312 |
| Eurycea guttolineata | JAXCLM000000000 | GSU 27313 |
| Eurycea paludicola | JAXIUV000000000 | GSU 27314 |
| Eurycea quadridigitata | JAWWME000000000 | GSU 27315 |
| Necturus beyeri | JAWWEL000000000 | GSU 27321 |
| Plethodon glutinosus | JAWWMG000000000 | GSU 27323 |
| Plethodon ventralis | JAWWEK000000000 | GSU 27322 |
| Pseudobranchus striatus | JAWWMD000000000 | GSU 27324 |
| Pseudotriton montanus | JAXIUS000000000 | GSU 27316 |
| Pseudotriton ruber | JAWWEI000000000 | GSU 27317 |
| Siren reticulata | JAWWEF000000000 | GSU 27318 |
| Siren sphagnicola | JAWWMF000000000 | GSU 27319 |
| Stereochilus marginatus | JAVXUN000000000 | GSU 27320 |
Funding
Funding was provided by Iridian Genomes grant# IRGEN_RG_2021-1345 “Genomic Studies of Eukaryotic Taxa” to SP, U.S. NSF grants DEB-1655737 to RAP and DEB-1656111 to DAB, GW UFF grants FY21 & FY23 to RAP, and an Andrew Sabin Family Foundation grant to RAP and TJC. Computing resources were graciously provided on the High Performance Computing Cluster operated by Research Technology Services at the George Washington University (MacLachlan et al. 2021), and the Smithsonian Institution High Performance Computing Cluster.
REFERENCES
- Bankevich Anton, Nurk Sergey, Antipov Dmitry, Gurevich Alexey A., Dvorkin Mikhail, Kulikov Alexander S., Lesin Valery M., et al. 2012. “SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.” Journal of Computational Biology 19 (5): 455–77. 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bolger Anthony M., Lohse Marc, and Usadel Bjoern. 2014. “Trimmomatic: A Flexible Trimmer for Illumina Sequence Data.” Bioinformatics 30 (15): 2114–20. 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Buckner JC, Sanders RC, Faircloth BC, and Chakrabarty P. 2021. “The Critical Importance of Vouchers in Genomics.” Elife 10: e68264. 10.7554/eLife.68264. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kieras M, O’Neill K, and Pirro S. 2021. Zanfona, a genome assembly finishing tool for paired-end Illumina reads. https://github.com/zanfona734/zanfona.
- Pyron RA, and Beamer DA. 2022a. “Allocation of Salamandra Auriculata Holbrook, 1838, with a New Species of Swamp-Dwelling Dusky Salamander (Plethodontidae: Desmognathus) from the Atlantic Coastal Plain.” Zootaxa 5188: 587–95. 10.11646/zootaxa.5188.6.6. [DOI] [PubMed] [Google Scholar]
- ———. 2022b. “Nomenclatural Solutions for Diagnosing ‘Cryptic’ Species Using Molecular and Morphological Data Facilitate a Taxonomic Revision of the Black-Bellied Salamanders (Urodela, Desmognathus ‘Quadramaculatus’) from the Southern Appalachian Mountains.” Bionomina 27: 1–43. 10.11646/bionomina.27.1.1. [DOI] [Google Scholar]
- ———. 2022c. “Systematics of the Ocoee Salamander (Plethodontidae: Desmognathus Ocoee), with Description of Two New Species from the Southern Blue Ridge Mountains.” Zootaxa 5190: 207–40. 10.11646/zootaxa.5190.2.3. [DOI] [PubMed] [Google Scholar]
- ———. 2023. “Systematic Revision of the Spotted and Northern Dusky Salamanders (Plethodontidae: Desmognathus Conanti and D. Fuscus), with Six New Species from the Eastern United States.” Zootaxa 5311 (4): 451–504. 10.11646/zootaxa.5311.4.1. [DOI] [PubMed] [Google Scholar]
- Pyron RA, O’Connell KA, Duncan S, Burbrink FT, and Beamer DA. 2023. “Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus Monticola).” Systematic Biology 72: 179–97. 10.1093/sysbio/syac065. [DOI] [PubMed] [Google Scholar]
- Pyron RA, O’Connell KA, Lamb JY, and Beamer DA. 2022. “A New, Narrowly Endemic Species of Swamp-Dwelling Dusky Salamander (Plethodontidae: Desmognathus) from the Gulf Coastal Plain of Mississippi and Alabama.” Zootaxa 5133: 53–82. 10.11646/zootaxa.5133.1.3. [DOI] [PubMed] [Google Scholar]