Abstract
Background
The genus Trichoglossus belongs to the family Psittacidae and includes fourteen species distributed worldwide. According to the International Union for Conservation of Nature and Natural Resources (IUCN) Red List of Threatened Species, most Trichoglossus species have shown a decreasing population trend recently. In particular, Trichoglossus forsteni is listed as “Endangered” in the IUCN Red List of Threatened Species. Moreover, Trichoglossus haematodus and Trichoglossus moluccanus are one of the most traded and illegally traded parrots. However, only a few genetic studies have been conducted regarding the conservation of this genus.
Methods and results
In the present study, complete mitochondrial genomes of three species (T. forsteni, T. haematodus, and T. moluccanus) were sequenced and compared with Trichoglossus rubritorquis, species whose mitochondrial genome is already reported. Results indicate that the complete mitochondrial genomes of the three species were similar in length (17,906 bp for T. haematodus to 17,909 bp for T. forsteni). Furthermore, the organization and order of these three mitochondrial genomes were identical, including thirteen protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two control regions (CRs) categorized into three domains containing nine conserved motifs. In addition, the genus Trichoglossus formed a well-supported monophyletic lineage.
Conclusions
The results of this study may be useful for future genetic studies toward the conservation of the genus Trichoglossus.
References
Blanco G, Hiraldo F, Tella JL (2018) Ecological functions of parrots: an integrative perspective from plant life cycle to ecosystem functioning. Emu-Austral Ornithol 118(1):36–49. https://doi.org/10.1080/01584197.2017.1387031
Olah G, Butchart SH, Symes A, Guzmán IM, Cunningham R, Brightsmith DJ, Heinsohn R (2016) Ecological and socio-economic factors affecting extinction risk in parrots. Biodivers Conserv 25(2):205–223. https://doi.org/10.1007/s10531-015-1036-z
Bush ER, Baker SE, Macdonald DW (2014) Global trade in exotic pets 2006–2012. Conserv Biol 28(3):663–676. https://doi.org/10.1111/cobi.12240
Scheffers BR, Oliveira BF, Lamb I, Edwards DP (2019) Global wildlife trade across the tree of life. Science 366(6461):71–76. https://doi.org/10.1126/science.aav5327
del Hoyo J (2020) All the Birds of the World. Lynx Edicions, Barcelona, p 381
BirdLife International (2022) IUCN Red List for birds. http://www.birdlife.org. Assessed 20 March 2022
Setiyani AD, Ahmadi MA (2020) An overview of illegal parrot trade in Maluku and North Maluku Provinces. For Soc 48–60. https://doi.org/10.24259/fs.v4i1.7316
Xu N, Zhang Q, Chen R, Liu H (2019) The complete mitogenome of red-collared lorikeet (Trichoglossus rubritorquis) and its phylogenetic analysis. Mitochondrial DNA B: Resour 4(2):3116–3117. https://doi.org/10.1080/23802359.2019.1667917
Kim J, Karagozlu MZ, An H, Choi T, Yeo Y, Kim C (2021) Development of polymorphic microsatellite markers for the Trichoglossus haematodus and cross-species amplification in Trichoglossus moluccanus. Mol Biol Rep 48(7):5787–5793. https://doi.org/10.1007/s11033-021-06555-y
Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27(8):1767–1780. https://doi.org/10.1093/nar/27.8.1767
Hebert PD, Cywinska A, Ball SL, Dewaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc B: Biol Sci 270(1512):313–321. https://doi.org/10.1098/rspb.2002.2218
Lee JC, Tsai L, Huang M, Jhuang J, Yao C, Chin S, Wang L, Linacre A, Hsieh H (2008) A novel strategy for avian species identification by cytochrome b gene. Electrophoresis 29(11):2413–2418. https://doi.org/10.1002/elps.200700711
Faria PJ, Guedes NM, Yamashita C, Martuscelli P, Miyaki CY (2008) Genetic variation and population structure of the endangered Hyacinth Macaw (Anodorhynchus hyacinthinus): implications for conservation. Biodivers Conserv 17(4):765–779. https://doi.org/10.1007/s10531-007-9312-1
Varela AI, Brokordt K, Ismar-Rebitz SM, Gaskin CP, Carlile N, O’Dwyer T, Adams J, VanderWerf EA, Luna‐Jorquera G(2020) Genetic diversity, population structure, and historical demography of a highly vagile and human‐impacted seabird in the Pacific Ocean: The red‐tailed tropicbird, Phaethon rubricauda. Aquat Conserv: Mar Freshwat Ecosyst 31(2):367 – 337. https://doi.org/10.1002/aqc.3471
Zardoya R, Meyer A (1996) Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol Biol Evol 13(7):933–942. https://doi.org/10.1093/oxfordjournals.molbev.a025661
Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res 41(13):e129. https://doi.org/10.1093/nar/gkt371
Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69(2):313–319. https://doi.org/10.1016/j.ympev.2012.08.023
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649. https://doi.org/10.1093/bioinformatics/bts199
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096
Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41(3):353–358. https://doi.org/10.1007/BF00186547
Eberhard JR, Wright TF, Bermingham E (2001) Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Mol Biol Evol 18(7):1330–1342
Ruokonen M, Kvist L (2002) Structure and evolution of the avian mitochondrial control region. Mol Phylogenet Evol 23(3):422–432
Lima NCB, Soares AER, Almeida, Luiz Gonzaga de Paula, Costa IRd, Sato FM, Schneider P, Aleixo A, Schneider MP, Santos FR, Mello CV(2018) Comparative mitogenomic analyses of Amazona parrots and Psittaciformes. Genetics and molecular biology 41(3):593–604. https://doi.org/10.1590/1678-4685-gmb-2017-0023
Kim J, Do TD, Choi Y, Yeo Y, Kim C (2021) Characterization and comparative analysis of complete mitogenomes of three Cacatua Parrots (Psittaciformes: Cacatuidae). Genes 12(2):209. https://doi.org/10.1093/oxfordjournals.molbev.a003917
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780. https://doi.org/10.1093/molbev/mst010
Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56(4):564–577. https://doi.org/10.1080/10635150701472164
Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B (2017) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol 34(3):772–773. https://doi.org/10.1093/molbev/msw260
Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539–542. https://doi.org/10.1093/sysbio/sys029
Nguyen L, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32(1):268–274. https://doi.org/10.1093/molbev/msu300
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67(5):901–904. https://doi.org/10.1093/sysbio/syy032
Chen Y (2019) The complete mitochondrial genome of yellow-bibbed lory, Lorius chlorocercus (Psittaciformes Psittacidae), with its phylogenetic relationship. Mitochondrial DNA Part B 4(2):3862–3863. https://doi.org/10.1080/23802359.2019.1687037
Guan X, Xu J, Smith EJ (2016) The complete mitochondrial genome sequence of the budgerigar, Melopsittacus undulatus. Mitochondrial DNA Part A 27(1):401–402. https://doi.org/10.3109/19401736.2014.898277
Eberhard JR, Wright TF (2016) Rearrangement and evolution of mitochondrial genomes in parrots. Mol Phylogenet Evol 94:34–46. https://doi.org/10.1016/j.ympev.2015.08.011
Urantówka AD, Kroczak A, Silva T, Padrón RZ, Gallardo NF, Blanch J, Blanch B, Mackiewicz P (2018) New insight into parrots’ mitogenomes indicates that their ancestor contained a duplicated region. Mol Biol Evol 35(12):2989–3009. https://doi.org/10.1093/molbev/msy189
Schweizer M, Wright TF, Peñalba JV, Schirtzinger EE, Joseph L (2015) Molecular phylogenetics suggests a New Guinean origin and frequent episodes of founder-event speciation in the nectarivorous lories and lorikeets (Aves: Psittaciformes). Mol Phylogenet Evol 90:34–48. https://doi.org/10.1016/j.ympev.2015.04.021
Braun MP, Reinschmidt M, Datzmann T, Zamora R, Neves L, Arndt T (2017) Influences of oceanic islands & the Pleistocene on the biogeography & evolution of two groups of Australasian parrots (Aves: Psittaciformes: Eclectus roratus, Trichoglossus haematodus complex). Rapid evolution & implications for taxonomy & conservation. Eur J Ecol 3(2):47–66. https://doi.org/10.1515/eje-2017-0014
Schirtzinger EE, Tavares ES, Gonzales LA, Eberhard JR, Miyaki CY, Sanchez JJ, Hernandez A, Müeller H, Graves GR, Fleischer RC (2012) Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes. Mol Phylogenet Evol 64(2):342–356. https://doi.org/10.1016/j.ympev.2012.04.009
Acknowledgements
Authors thank Seoul Zoo for helping with the supplement sample. The samples collection was conducted with the assistance of So Young Jung, Jung Yeol An, In Hui Park, Han Sol Kim, Su Yeon Seo, Mihyun Yoo, and Hany Lee.
Funding
This work was supported by Korea Environment Industry & Technology Institute (KEITI) through Public Technology Program based on Environmental Policy, funded by Korea Ministry of Environment (MOE) (2018000210004).
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J.I.K. and C.B.K. conceptualized the study, J.I.K., T.D.D and Y.Y. performed the experiments and analyzed data, J.I.K. and C.B.K. wrote the first draft of manuscript, C.B.K. revised the final draft of manuscript.
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Ethical clearance for the present study was permitted by the Institutional Animal Care and Use Committee (IACUC) of Seoul Zoo (Number: 2019-001). All sampling was according to the standard protocols of this committee.
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Kim, JI., Do, T.D., Yeo, Y. et al. Comparative analysis of complete mitochondrial genomes of three Trichoglossus species (Psittaciformes: Psittacidae). Mol Biol Rep 49, 9121–9127 (2022). https://doi.org/10.1007/s11033-022-07791-6
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DOI: https://doi.org/10.1007/s11033-022-07791-6