Capurucho, João Marcos G., Taylor Hains, Stacy Pirro, John Bates, and Shannon
Hackett. 2023. “The Complete Genome Sequences of 19 Species of Snipes(Scolopacidae, Charadriiformes, Aves).” Biodiversity Genomes, April.
https://doi.org/10.56179/001c.74632.

GENOME SEQUENCING

The Complete Genome Sequences of 19 Species of Snipes(Scolopacidae, Charadriiformes, Aves)
João Marcos G. Capurucho1,2, Taylor Hains3,4, Stacy Pirro5, John Bates3, Shannon Hackett3
1 Coordenação de Biodiversidade, Field Museum of Natural History, 2 Committee on Evolutionary Biology, Instituto Nacional de Pesquisas da Amazônia,3 Negaunee Integrative Research Center, Field Museum of Natural History, 4 University of Chicago, Committee on Evolutionary Biology, 5 Biodiversity, Iridian

Genomes
Keywords: bird, genome
https://doi.org/10.56179/001c.74632

Biodiversity Genomes
We present the complete genome sequences of 19 species of snipes from 7 genera.
Illumina sequencing was performed on genetic material from museumspecimens. The reads were assembled using a de novo method followed by afinishing step. The raw and assembled data are publicly available via Genbank.

Introduction
Snipes (Scolopacidae) include 97 extant species (Lepage, Vaidya, and Guralnick
2014; Winkler, Billerman, and Lovette 2020). We present the assembled
genomes of 19 species from this family. Tissues were obtained from vouchered
museum specimens. More detailed information about the specimen used foreach species can be found in the Biosample linked to each genome assembly in
Genbank.

Methods
DNA extraction was performed using the Qiagen DNAeasy genomic
extraction kit using the standard protocol. A paired-end sequencing library
was constructed using the Illumina TruSeq kit according to the manufacturer’sinstructions. The library was sequenced on an Illumina Hi-Seq platform inpaired-end, 2 × 150 bp format. The resulting fastq files were trimmed ofadapter/primer sequence and low-quality regions with Trimmomatic v0.33(Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled bySPAdes v2.5 (Bankevich et al. 2012) followed by a finishing step using Zanfona(Kieras, O’Neill, and Pirro 2021).

Results and Data Availability
All data, including raw reads and assembled genome sequence, is available viaGenbank.

The Complete Genome Sequences of 19 Species of Snipes (Scolopacidae, Charadriiformes, Aves)

Bartramia longicauda

JAOXNH000000000

Calidris melanotos

JAOWAO000000000

Gallinago delicata

JAOQGJ000000000

Gallinago gallinago

JAOQMJ000000000

Gallinago hardwickii

JAOQGE000000000

Gallinago jamesoni

JAOQGH000000000

Gallinago media

JAOSLN000000000

Gallinago megala

JAOQGF000000000

Gallinago nigripennis

JAOQGL000000000

Gallinago paraguaiae

JAOSZB000000000

Gallinago solitaria

JAOQGI000000000

Gallinago stenura

JAOQGM000000000

Gallinago undulata

JAOTQQ000000000

Limnodromus scolopaceus

JAOXNO000000000

Scolopax bukidnonensis

JAOWAV000000000Scolopax minor

JAOXNG000000000

Scolopax rusticola

JAOWAS000000000

Tringa solitaria

JAOXJM000000000

Xenus cinereus

JAOXJK000000000

Funding
Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345
Genomic Studies of Eukaryotic Taxa.
Submitted: April 10, 2023 EDT, Accepted: April 21, 2023 EDT

Biodiversity Genomes

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The Complete Genome Sequences of 19 Species of Snipes (Scolopacidae, Charadriiformes, Aves)referencesBankevich, Anton, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander
S. Kulikov, Valery M. Lesin, et al. 2012. “SPAdes: A New Genome Assembly Algorithm and Its
Applications to Single-Cell Sequencing.” Journal of Computational Biology 19 (5): 455–77.
https://doi.org/10.1089/cmb.2012.0021.
Bolger, Anthony M., Marc Lohse, and Bjoern Usadel. 2014. “Trimmomatic: A Flexible Trimmer for
Illumina Sequence Data.” Bioinformatics 30 (15): 2114–20. https://doi.org/10.1093/
bioinformatics/btu170.
Kieras, M., K. O’Neill, and S. Pirro. 2021. Zanfona, a genome assembly finishing tool for paired-end
Illumina reads. https://github.com/zanfona734/zanfona.
Lepage, Denis, Gaurav Vaidya, and Robert Guralnick. 2014. “Avibase – a Database System forManaging and Organizing Taxonomic Concepts.” Zookeys 420 (June): 117–35. https://doi.org/10.3897/zookeys.420.7089.
Winkler, David W., Shawn M. Billerman, and Irby J. Lovette. 2020. “Sandpipers and Allies(Scolopacidae).” In Birds of the World, edited by Shawn M. Billerman, Brooke K. Keeney, Paul G.
Rodewald, and Thomas S. Schulenberg. Cornell Lab of Ornithology. https://doi.org/10.2173/bow.scolop2.01.

Biodiversity Genomes3