Abstract
We present complete genome sequences of 23 species of finches from 6 genera.
Introduction
Birds in the Fringillidae family are true finches. There are three subfamilies, Fringillinae, Euphoniinae and Carduelinae (Zuccon et al. 2012). They are small to medium-sized, widespread, largely granivorous birds and are native to every continent except Antarctica and Australia. They also have colonized and differentiated on oceanic islands. They often have stout, conical-shaped bills (except Hawaiian honeycreepers) (Winkler, Billerman, and Lovette 2015). Some of European origin have been introduced to Australia and New Zealand. There are also introduced populations across the world, including in the United States and Argentina, where they share geography with native finches (North and South American siskins, redpolls, rosefinches etc.). Several species are common caged birds and historically have been kept as pets (e.g. European Goldfinches) or for human services (e.g. Canaries to detect carbon monoxide in coal mines).
Methods
Tissues 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 | Genome | Specimen_voucher |
|---|---|---|
| Acanthis cabaret | JAUYWM000000000 | FMNH 177662 |
| Acanthis flamea | JAYJLY000000000 | FMNH 95021 |
| Carduelis citrinella | JAYRBP000000000 | FMNH 343157 |
| Carduelis corsicana | JAUYWN000000000 | FMNH 343161 |
| Linurgus olivaceus | JAYRCA000000000 | FMNH 298894 |
| Loxia leucoptera | JAWWMI000000000 | FMNH 328157 |
| Loxia pytyopsittacus | JAUYWL000000000 | FMNH 126802 |
| Serinus cacnicollis | JAUUDU000000000 | FMNH 441104 |
| Serinus flavivertex | JAYDBR000000000 | FMNH 83958 |
| Serinus nigriceps | JAUZTC000000000 | FMNH 83996 |
| Serinus pusillus | JAYRBO000000000 | FMNH 66471 |
| Serinus serinus | JAVCKY000000000 | FMNH 185003 |
| Serinus syriacus | JAWWMM000000000 | FMNH 343155 |
| Spinus atriceps | JAVRMD000000000 | FMNH 189863 |
| Spinus crassirostris | JAYRBZ000000000 | FMNH 391990 |
| Spinus lawrencei | JAUZTD000000000 | FMNH 177750 |
| Spinus olivaceus | JAYRCE000000000 | FMNH 481061 |
| Spinus pinus | JAUUDX000000000 | FMNH 437097 |
| Spinus psaltria | JAYJLW000000000 | FMNH 121653 |
| Spinus spinescens | JAUYUU000000000 | FMNH 220593 |
| Spinus spinus | JAUUDX000000000 | FMNH 185006 |
| Spinus tristis | JAYRBQ000000000 | FMNH 495559 |
| Spinus yarrellii | JAYDZH000000000 | FMNH 53368 |
Funding
Funding was provided by Iridian Genomes grant# IRGEN_RG_2021-1345 “Genomic Studies of Eukaryotic Taxa.
REFERENCES
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