Methods

Tissues from single, wild-collected individuals were used for this study.

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:

Species Accession Specimen_voucher
Amazonetta brasiliensis JBBYHF000000000 UAM Bird:14628
Anas acuta JAYRCF000000000 ANSP tissue:28083
Anas aucklandica JBCATX000000000 ANSP skin:77177
Anas bahamensis JBBYHN000000000 UAM Bird:36736
Anas bernieri JAUEKP000000000 SHbern_V68VBK8SIL
Anas capensis JAUELN000000000 REW671
Anas carolinensis JBCAUC000000000 ANSP skin:189308
Anas crecca JAYJLT000000000 ANSP tissue:27782
Anas flavirostris JBCATY000000000 UAM Bird:24711
Anas georgica JAUBNX000000000 KGM274
Anas poecilorhyncha JBCJKG000000000 ANSP skin:128732
Anas puna JBBYGV000000000 UAM Bird:38306
Anas zonorhyncha JBCAUD000000000 ANSP skin:85306
Lophonetta specularioides JAUJPM000000000 KGM821
Mareca americana JAXIUU000000000 ANSP tissue:22592
Mareca falcata JBBYGQ000000000 UAM Bird:21189
Mareca penelope JAYRCD000000000 ANSP tissue:27964
Mareca sibilatrix JAVKLD000000000 REW261
Sibirionetta formosa JBCAUB000000000 UAM Bird:28790
Spatula clypeata JBCATZ000000000 ANSP skin:190948
Spatula discors JAUJPJ000000000 REW001
Spatula querquedula JAUJPN000000000 UWBM 36215
Spatula rhynchotis JAVKLC000000000 UWBM 78156
Spatula smithii JAWDEW000000000 REW674
Spatula versicolor JBBYHG000000000 UAM Bird:17529
Speculanas specularis JAUJTY000000000 KGM271
Tachyeres brachypterus JAULBN000000000 REW330
Tachyeres leucocephalus JAVDPI000000000 KGM823
Tachyeres patachonicus JBBYHP000000000 UAM Bird:20714

Funding

Funding was provided by Iridian Genomes grant# IRGEN_RG_2021-1345: Genomic Studies of Eukaryotic Taxa.