The Draft Genome Sequences of 50 Salamander species (Caudata, Amphibia)

R. Alexander Pyron; Stacy Pirro; Taylor Hains; Timothy J. Colston; Edward A. Myers; Kyle A. O’Connell; David A. Beamer

doi:10.56179/001c.116891

Pyron, R. Alexander, Stacy Pirro, Taylor Hains, Timothy J. Colston, Edward A. Myers, Kyle A. O’Connell, and David A. Beamer. 2024. “The Draft Genome Sequences of 50 Salamander Species (Caudata, Amphibia).” Biodiversity Genomes, April. https://doi.org/10.56179/001c.116891.

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Abstract

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.

Submitted: April 22, 2024 EDT

Accepted: April 23, 2024 EDT

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