De-novo Assembly of Four Rail (Aves: Rallidae) Genomes: A Resource for Comparative Genomics

Overview

Journal Ecol Evol

Date 2024 Jul 19

PMID 39026944

Authors

Julien Gaspar

Steve A Trewick

Gillian C Gibb

Affiliations

Soon will be listed here.

Abstract

Rails are a phenotypically diverse family of birds that includes 130 species and displays a wide distribution around the world. Here we present annotated genome assemblies for four rails from Aotearoa New Zealand: two native volant species, pūkeko and mioweka , and two endemic flightless species takahē and weka . Using the sequence read data, heterozygosity was found to be lowest in the endemic flightless species and this probably reflects their relatively small populations. The quality checks and comparison with other rallid genomes showed that the new assemblies were of good quality. This study significantly increases the number of available rallid genomes and will enable future genomic studies on the evolution of this family.

References

Lanfear R, Frandsen P, Wright A, Senfeld T, Calcott B . PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Mol Biol Evol. 2016; 34(3):772-773. DOI: 10.1093/molbev/msw260. View

Grueber C, Laws R, Nakagawa S, Jamieson I . Inbreeding depression accumulation across life-history stages of the endangered Takahe. Conserv Biol. 2010; 24(6):1617-25. DOI: 10.1111/j.1523-1739.2010.01549.x. View

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

Chen S, Zhou Y, Chen Y, Gu J . fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34(17):i884-i890. PMC: 6129281. DOI: 10.1093/bioinformatics/bty560. View

Garcia-R J, Gibb G, Trewick S . Eocene diversification of crown group rails (Aves: Gruiformes: Rallidae). PLoS One. 2014; 9(10):e109635. PMC: 4188725. DOI: 10.1371/journal.pone.0109635. View

Seppey M, Manni M, Zdobnov E . BUSCO: Assessing Genome Assembly and Annotation Completeness. Methods Mol Biol. 2019; 1962:227-245. DOI: 10.1007/978-1-4939-9173-0_14. View

Ewing B, Green P . Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998; 8(3):186-94. View

Trewick S, Pilkington S, Shepherd L, Gibb G, Morgan-Richards M . Closing the gap: Avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response. Mol Ecol. 2017; 26(20):5752-5772. DOI: 10.1111/mec.14323. View

Chapman J, Ho I, Sunkara S, Luo S, Schroth G, Rokhsar D . Meraculous: de novo genome assembly with short paired-end reads. PLoS One. 2011; 6(8):e23501. PMC: 3158087. DOI: 10.1371/journal.pone.0023501. View

10.

Ewing B, Hillier L, Wendl M, Green P . Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998; 8(3):175-85. DOI: 10.1101/gr.8.3.175. View

11.

Fain M, Krajewski C, Houde P . Phylogeny of "core Gruiformes" (Aves: Grues) and resolution of the Limpkin-Sungrebe problem. Mol Phylogenet Evol. 2007; 43(2):515-29. DOI: 10.1016/j.ympev.2007.02.015. View

12.

Garcia-R J, Gibb G, Trewick S . Deep global evolutionary radiation in birds: diversification and trait evolution in the cosmopolitan bird family Rallidae. Mol Phylogenet Evol. 2014; 81:96-108. DOI: 10.1016/j.ympev.2014.09.008. View

13.

Baker A, Daugherty C, Colbourne R, McLennan J . Flightless brown kiwis of New Zealand possess extremely subdivided population structure and cryptic species like small mammals. Proc Natl Acad Sci U S A. 1995; 92(18):8254-8. PMC: 41135. DOI: 10.1073/pnas.92.18.8254. View

14.

Burga A, Wang W, Ben-David E, Wolf P, Ramey A, Verdugo C . A genetic signature of the evolution of loss of flight in the Galapagos cormorant. Science. 2017; 356(6341). PMC: 5567675. DOI: 10.1126/science.aal3345. View

15.

Trewick S . Flightlessness and phylogeny amongst endemic rails (Aves:Rallidae) of the New Zealand region. Philos Trans R Soc Lond B Biol Sci. 1997; 352(1352):429-46. PMC: 1691940. DOI: 10.1098/rstb.1997.0031. View

16.

Chikhi R, Medvedev P . Informed and automated k-mer size selection for genome assembly. Bioinformatics. 2013; 30(1):31-7. DOI: 10.1093/bioinformatics/btt310. View

17.

Wu T, Watanabe C . GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005; 21(9):1859-75. DOI: 10.1093/bioinformatics/bti310. View

18.

Richterich P . Estimation of errors in "raw" DNA sequences: a validation study. Genome Res. 1998; 8(3):251-9. PMC: 310698. DOI: 10.1101/gr.8.3.251. View

19.

Gaspar J, Gibb G, Trewick S . Convergent morphological responses to loss of flight in rails (Aves: Rallidae). Ecol Evol. 2020; 10(13):6186-6207. PMC: 7381585. DOI: 10.1002/ece3.6298. View

20.

Steadman D . Prehistoric extinctions of pacific island birds: biodiversity meets zooarchaeology. Science. 1995; 267(5201):1123-31. DOI: 10.1126/science.267.5201.1123. View