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Mitochondrial DNA B Resour
Mitochondrial DNA B Resour
Mitochondrial DNA. Part B, Resources
2380-2359
Taylor & Francis

10.1080/23802359.2024.2397980
2397980
Version of Record
Data Note
Mitogenome Report
The complete mitochondrial genome of aglaeactis castelnaudii (bourcier & mulsant, 1848) (apodiformes: trochilidae: aglaeactis) and phylogenetic analysis
G. Liu et al.
Liu Guangshuai
Liu Jincheng
Zhang Xinyue
https://orcid.org/0000-0003-2660-7882
Gao Xiaodong
College of Life Science, Qufu Normal University, Qufu, PR China
Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2397980.

CONTACT Xiaodong Gao gao-xiaodong@163.com College of Life Science, Qufu Normal University, Qufu 273165, Shandong, China.
4 9 2024
2024
4 9 2024
9 9 11811184
13 5 2024
24 8 2024
KnowledgeWorks Global Ltd.3 9 2024
published online in a building issue3 9 2024
© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
2024
The Author(s)
https://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

Abstract

In this study, we employed high-throughput sequencing data to assemble the mitochondrial genome (mitogenome) of the White-tufted Sunbeam (Aglaeactis castelnaudii). The total length of the mitogenome was found to be 16,872 base pairs (bp), containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The nucleotide composition was as follows: A 30.6%, T 24.0%, C 31.2%, and G 14.2%, resulting in a GC content of 45.4%. Phylogenetic analysis, utilizing the concatenation of the 13 mitochondrial PCGs, indicated a closer evolutionary relationship between the genus Aglaeactis and the genus Coeligena compared to other genera within the family Trochilidae investigated in this study. The mitogenome of A. castelnaudii not only contributes to species identification but also provides valuable insights for phylogenetic and conservation genetic analyses of A. castelnaudii.

Keywords

Aglaeactis castelnaudii
mitochondrial genome
phylogenetic analysis
National Natural Science Foundation of China 10.13039/501100001809 32200407 This research was supported by the National Natural Science Foundation of China [32200407].
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pmcIntroduction

The White-tufted Sunbeam, scientifically known as Aglaeactis castelnaudii (Figure 1), belongs to the hummingbird family Trochilidae. A. castelnaudii inhabits a restricted and fragmented range, exclusively found in the Andes of Peru, Bolivia, and Northern Chile. It prefers damp montane forests and high-altitude shrublands in subtropical or tropical regions (Parker & O'Neill 1980). Playing a significant role in ecosystem regulation, A. castelnaudii primarily feeds on insects or flower nectar from blooming plants in its Andean habitat (Watts 2008). The International Union for Conservation of Nature (IUCN) describes this species as 'common but patchily distributed’ within its habitat, although an accurate estimation of the overall population is currently lacking. As of 2017, the White-tufted Sunbeam is classified as ‘Near Threatened’ (NT) on the IUCN Red List, with its population size and trend assessed as ‘Decreasing’ (BirdLife International 2017).

Figure 1. Image of an adult individual of aglaeactis castelnaudii (photo credit: David F. Belmonte, email: david.rguezpascual@gmail.com, used with permission). This photograph was captured in october 2022 in grau apurímac, Peru. The original photograph is accessible to the public on iNaturalist (https://www.inaturalist.org/photos/250606396?size=original).

The genus Aglaeactis comprises four species (Schuchmann 1985) and belongs to the Andean hummingbird clade (McGuire et al. 2014). All Aglaeactis hummingbirds inhabit the high Andes at elevations ranging from 2500 to 4300 m, where they have evolved several distinct adaptive phenotypes to survive in this challenging environment (Schuchmann 1990; Ocampo et al. 2020). Consequently, this group stands as a notable example of adaptive radiation in temperate and high latitudes. Remarkably, the genus Aglaeactis remains among the least researched hummingbird genera globally, with the mitogenome of this genus yet to undergo sequencing. In this study, we present and elucidate the mitogenome of A. castelnaudii for the first time. This study offers genetic data crucial for future studies into species identification, biodiversity surveillance, conservation genetics, and investigations into adaptive evolution.

Materials and methods

In this study, the mitogenome of A. castelnaudii was assembled utilizing publicly available high-throughput genomic data in NCBI, which was submitted by the Sam Noble Oklahoma Museum of Natural History. An individual muscle tissue sample from A. castelnaudii was collected in Peru, situated at coordinates 14.058 S latitude and 73.001 W longitude. This sample was preserved at the Sam Noble Oklahoma Museum of Natural History (https://samnoblemuseum.ou.edu/, contact person: Jessica McLaughlin, email: jfmclaughlin@berkeley.edu) under the sample label ca169414. Genomic DNA was isolated from the muscle tissue and subjected to sequencing on an Illumina NovaSeq 6000 platform utilizing 150 bp paired-end runs (2 × 150). The genomic data supporting the findings of this study can be accessed at NCBI's Sequence Read Archive (SRA) via the following link: https://www.ncbi.nlm.nih.gov/sra/, with the accession number SRR19461672. Data collection was conducted in compliance with the IUCN policies research involving species at risk of extinction (see Guidelines for appropriate uses of IUCN Red list data). Furthermore, we adhered to the regulations of Convention on Biological Diversity and the Convention on the Trade in Endangered Species of Wild Fauna and Flora.

We extracted the mitochondrial reads from the genomic data and proceeded to perform assembly using MitoZ v3.6 (Meng et al. 2019). After a manual examination, the resulting mitogenome was annotated and visually displayed using Proksee (Grant et al. 2023) (https://proksee.ca/). The nucleotide sequences of each PCG of A. castelnaudii and its related species were aligned using MUSCLE v3.8.31 (Edgar 2004). The best-fit substitution model for each alignment was determined using the ModelFinder model (Kalyaanamoorthy et al. 2017) integrated within IQ-TREE2 (Nguyen et al. 2015). Phylogenetic analysis using Maximum Likelihood (ML) of A. castelnaudii and other species of hummingbirds and one outgroup (Apus apus) was performed using IQ-TREE2 (Nguyen et al. 2015) based on the sequences from 13 mitochondrial protein-coding genes (PCGs). Individual gene alignments were combined to form a partitioned supermatrix encompassing 11,385 bp. This supermatrix was then employed to construct a ML tree with separate model partitions for each gene. The reliability of the branches within the tree was evaluated using UFBoot2 (Hoang et al. 2018) with 1,000 bootstrap replicates.

Results

The complete mitogenome of A. castelnaudii spans 16,872 bp (NCBI accession number: PP754509). The average read depth coverage for the mitogenome reached 902.9 × (Fig. S1). The mitogenome consists of 13 PCGs, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a single control region referred to as the D-loop (Figure 2). This genetic arrangement adheres to the typical structure of avian mitochondrial genes. The nucleotide composition of the genome is as follows: Adenine (A) 30.6%, Thymine (T) 24.0%, Cytosine (C) 31.2%, and Guanine (G) 14.2%, demonstrating a slight bias toward AT content at 54.6%. Notably, among the PCGs, ND5 is the longest, spanning 1,815 bp, while ATP8 is the shortest at 168 bp. The two rRNA genes (12S rRNA and 16S rRNA) are 974 bp and 1,592 bp in length respectively, positioned between tRNAPhe and tRNALeu, and separated by the tRNAVal gene. Furthermore, this genomic configuration encompasses 22 transfer RNAs (tRNAs) with lengths ranging from 67 to 80 bp.

Figure 2. The mitogenome map of aglaeactis castelnaudii, drawn by using proksee (Grant et al. 2023) (https://proksee.ca/). GC content was also shown in the figure.

Discussion and conclusion

We assembled and reported the first complete mitogenome of A. castelnaudii based on high-throughput genomic data. The genomic orientation, gene arrangement, and nucleotide composition were very similar to other hummingbirds from the genera Archilochus (Morgan-Richards et al. 2008), Chrysolampis (Souto et al. 2016), and Amazilia (Prosdocimi et al. 2016). The A + T content of A. castelnaudii was 54.6%, consistent with the slight A + T bias observed in other hummingbird mitogenomes (Souto et al. 2016).

The phylogenetic tree supports a closer relationship between A. castelnaudii and Coeligena bonapartei compared to other species within the Trochilidae family investigated in this study (Figure 3). This contrasts with earlier phylogenetic analyses relying on four nuclear and two mitochondrial genes, which positioned C. bonapartei in a closer relationship with Heliodoxa aurescens, rather than with A. castelnaudii (McGuire et al. 2014). However, the respective topologies in both McGuire et al. (2014) and our study were both poorly supported, and thus require further research. Fundamentally, our study provides a valuable genetic resource for future investigations into the evolutionary trajectory and phylogenetic position of this distinctive hummingbird species exclusively found in the Andes.

Figure 3. Phylogenetic tree of 14 species belonging to the trochilidae family constructed by using the maximum likelihood (ML) method, utilizing a dataset consisting of 13 PCGs. Apus apus from family apodidae was used as outgroup. Bootstrap values were shown alongside to the branches. The following sequences were used to infer the tree: Amazilia brevirostris KP722043.1, archilochus colubris EF532935.1 (Morgan-Richards et al. 2008), calliphlox amethystine KP853095.1, calypte anna MN356119 (Feng et al. 2020), chrysolampis mosquitus KJ619585.1 (Souto et al. 2016), coeligena bonapartei MT341536.1 (Palacios et al. 2023), florisuga fusca KP853096.1, glaucis hirsutus KT265275.1, heliodoxa aurescens KP853094.1, hylocharis cyanus KJ619586.1, lophornis magnificus KT265276.1, oreotrochilus melanogaster KJ619587.1, phaethornis malaris KP853097.1, Apus apus NC_008540.1 (Slack et al. 2007), and aglaeactis castelnaudii PP754509.

Supplementary Material

Fig S1.tif

Author contributions

Guangshuai Liu and Xiaodong Gao designed this work and wrote the manuscript. Jincheng Liu and Xinyue Zhang assembled and annotated the mitochondrial genome. All authors agree to be accountable for all aspects of the work.

Ethical approval

This study did not raise any ethical issues as the mitogenome of A. castelnaudii was assembled using high-throughput genomic data previously sequenced by other research team. No animal experiments or sampling procedures were conducted in our study.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genomic data used for assembling the mitochondrial genome of A. castelnaudii are openly available in SRA of NCBI (https://www.ncbi.nlm.nih.gov/sra/) under the accession number SRR19461672. The associated BioProject and BioSample numbers are PRJNA844086 and SAMN28788517, respectively. Mitogenome of A. castelnaudii can be accessed via accession number PP754509 in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/PP754509.
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