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Genome Sequencing
April 23, 2024 EDT

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,
https://doi.org/10.56179/001c.116891
biogenomes
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

References

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