Research articles

Plastid Genome and Phylogenetic Analysis of Psychopsis sanderae

  • 许 静,潘仁富,黄思铭,黄卫昌,李明河
Expand
  • (1. College of Landscape and Art, Fujian Agriculture and Forestry University, Fuzhou 350108, Fujian China; 2. Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China)

Received date: 2025-03-29

  Accepted date: 2025-04-22

  Online published: 2025-12-17

Abstract

Using the leaves of the ornamental orchid Psychopsis sanderae as materials, based on high-throughput sequencing technology, the complete plastid genome of this species was assembled and annotated, and its plastid genome characteristics and phylogenetic position were analyzed. The results showed that the plastid genome of P. sanderae was 143 932 bp in size, presenting a circular quadripartite structure, with a GC content of 37.1%. A total of 127 genes were annotated, including 74 protein-coding genes, 38 transfer RNAs (tRNAs) genes, 8 ribosomal RNAs (rRNAs) genes and 7 pseudo genes. Among them, the entire lineage of the ndh gene family was pseudogenized or lost. The boundaries of the inverted repeat (IR) regions were highly conserved. The junction of the large single copy (LSC) region and the IRb region was located within the rpl22 gene, and the junction of the small single copy (SSC) region and the IRa region was located within the ycf1 gene. A total of 44 simple sequence repeats (SSRs) loci were detected, among which the mononucleotide repeats with adenine (A) or thymine (T) were the most abundant, accounting for 70.45%. Six high-variation hotspots of nucleotide polymorphism were obtained: trnQUUG, trnEUUC, trnSGGA, rps18, rps12, and rpl16. Phylogenetic analyses placed P. sanderae at the basal position within the subtribe Oncidiinae. This study provides the first comprehensive characterization of the plastid genome for P. sanderae, laying a foundation for future molecular marker development and phylogenetic studies of Psychopsis and its relatives.

Cite this article

许 静,潘仁富,黄思铭,黄卫昌,李明河 . Plastid Genome and Phylogenetic Analysis of Psychopsis sanderae[J]. Subtropical Plant Science, 2025 , 54(5) : 487 -496 . DOI: 10.3969/j.issn.1009-7791.2025.05.001

References

[1] Pridgeon A M, Cribb P J, Chase M C, Rasmussen F N. Epidendroideae (Part 2): Genera Orchidacearum [M]. Oxford: Oxford University Press, 2009, 5: 1–585.
[2] Rafinesque C S. Flora Telluriana [M]. Philadelphia: H. Probasco, 1838: 135.
[3] Swartz O P. Kongl [J]. VetenskapsAcademiens Nya Handlingar, 1800, 2(21): 239–240.
[4] Lückel E, Braem G J. Psychopsis und Psychopsiella: Eine alte und eine neue Gattung der Oncidium-Verwandtschaft [J]. Die Orchidee, 1982, 33(1): 1–7.
[5] Neubig K M, Whitten W M, Williams N H, Blanco M A, Endara L, Burleigh J G, Silvera K, Cushman J C, Chase M W. Generic recircumscriptions of Oncidiinae (Orchidaceae: Cymbidieae) based on maximum likelihood analysis of combined DNA datasets [J]. Botanical Journal of the Linnean Society, 2012, 168(2): 117–146.
[6] Givnish T J, Spalink D, Ames M, Lyon S P, Hunter S J, Zuluaga A, Iles W J D, Clements M A, Arroyo M T K, Leebens-Mack J, Endara L, Kriebel R, Neubig K M, Whitten W M, Williams N H, Cameron K M. Orchid phylogenomics and multiple drivers of their extraordinary diversification [J]. Proceedings of the Royal Society B: Biological Sciences, 2015, 282(1814): 20151553.
[7] Li Y X, Li Z H, Schuiteman A, Chase M W, Li J W, Huang W C, Hidayat A, Wu S S, Jin X H. Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes [J]. Molecular Phylogenetics and Evolution, 2019, 139: 106540.
[8] Niu Z T, Pan J J, Zhu S Y, Li L D, Xue Q Y, Liu W, Ding X Y. Comparative analysis of the complete plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) reveals different evolutionary dynamics of IR/SSC boundary among photosynthetic orchids [J]. Frontiers in Plant Science, 2017, 8: 1713.
[9] Delannoy E, Fujii S, Colas des Francs-Small C, Brundrett M, Small I. Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes [J]. Molecular Biology and Evolution, 2011, 28(7): 2077–2086.
[10] Allen G C, Flores-Vergara M A, Krasynanski S, Kumar S, Thompson W F. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide [J]. Nature Protocols, 2006, 1(5): 2320–2325.
[11] Andrews S. FastQC: a quality control tool for high throughput sequence data [J]. Bioinformatics, 2010, 26(15): 1968–1971.
[12] Jian J J, Yu W B, Yang J B, Song Y, dePamphilis C W, Yi T S, Li D Z. GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data [J]. BioRxiv, 2018: 256479.
[13] Wick R R, Schultz M B, Zobel J, Holt K E. Bandage: interactive visualization of de novo genome assemblies [J]. Bioinformatics, 2015, 31(20): 3350–3352.
[14] Qu X J, Moore M J, Li D Z, Yi T S. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes [J]. Plant Methods, 2019, 15: 1–12.
[15] Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Meintjes P, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data [J]. Bioinformatics, 2012, 28(12): 1647–1649.
[16] Greiner S, Lehwark P, Bock R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes [J]. Nucleic Acids Research, 2019, 47(W1): W59–W64.
[17] Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA–web: a web server for microsatellite prediction [J]. Bioinformatics, 2017, 33(16): 2583–2585.
[18] Amiryousefi A, Hyv?nen J, Poczai P. IRscope: an online program to visualize the junction sites of chloroplast genomes [J]. Bioinformatics, 2018, 34(17): 3030–3031.
[19] Brudno M, Malde S, Poliakov A, Do C B, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment [J]. Bioinformatics, 2003, 19(s1): i54–i62.
[20] Darling A C E, Mau B, Blattner F R, Perna N T. Mauve: multiple alignment of conserved genomic sequence with rearrangements [J]. Genome Research, 2004, 14(7): 1394–1403.
[21] Chase M W, Cameron K M, Freudestein J V, Pridgeon A M, Salazar G, Van den Berg C, Schuiteman A. An update classification of Orchidaceae [J]. Botanical Journal of the Linnean Society, 2015, 177(2): 151–174.
[22] Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform [J]. Nucleic Acids Research, 2002, 30(14): 3059–3066.
[23] Capella-Gutiérrez S, Silla-Martínez J M, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses [J]. Bioinformatics, 2009, 25(15): 1972–1973.
[24] Minh B Q, Schmidt H A, Chernomor O, Schrempf D, Woodhams M D, von Haeseler A, Lanfear R. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era [J]. Molecular Biology and Evolution, 2020, 37(5): 1530–1534.
[25] Kalyaanamoorthy S, Minh B Q, Wong T K F, von Haeseler A, Jermiin L S. ModelFinder: fast model selection for accurate phylogenetic estimates [J]. Nature Methods, 2017, 14(6): 587–589.
[26] Kim Y K, Jo S, Cheon S H, Kwak M, Kim Y D, Kim K J. Plastome evolution and phylogeny of subtribe Aeridinae (Vandeae, Orchidaceae) [J]. Molecular Phylogenetics and Evolution, 2020, 144: 106721.
[27] Niu Z T, Zhu S Y, Pan J J, Li L D, Jing S, Ding X Y. Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots [J]. Scientific Reports, 2017, 7(1): 2073.
[28] Chen Y Q, Zhong H, Zhu Y T. Plastome structure and adaptive evolution of Calanthe s. l. species [J]. PeerJ, 2020, 8: e10051.
[29] Zavala-Páez M, Vieira L N, Baura V A, Balsanelli E, Souza E M, Cevallos M, Chase M W, Smidt E. Comparative plastid genomics of neotropical Bulbophyllum (Orchidaceae; Epidendroideae) [J]. Frontiers in Plant Science, 2020, 11: 799.
[30] Pan I C, Liao D C, Wu F H, Daniell H, Singh N D, Chang C, Shih M C, Chan M T, Lin C S. Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding [J]. PLoS One, 2012, 7(4): e34738.
[31] Kim H T, Kim J S, Moore M J, Neubig K M, Williams N H, Whitten W M, Kim J H. Seven new complete plastome sequences reveal rampant independent loss of the ndh gene family across orchids and associated instability of the inverted repeat/small single-copy region boundaries [J]. PLoS One, 2015, 10(11): e0142215.
[32] Qu X J, Zhang X J, Cao D L, Guo X X, Mower J P, Fan S J. Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes [J]. Molecular Phylogenetics and Evolution, 2022, 174: 107544.
[33] Ruhlman T A, Zhang J, Blazier J C, Saber J S M, Jansen R K. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure [J]. American Journal of Botany, 2017, 104(4): 559–572.
[34] Zhou C Y, Lin W J, Li R Y, Wu Y H, Liu Z J, Li M H. Characterization of Angraecum (Angraecinae, Orchidaceae) plastomes and utility of sequence variability hotspots [J]. International Journal of Molecular Sciences, 2023, 25(1): 184.
[35] Gu C H, Ma L, Wu Z Q, Chen K, Wang Y X. Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales [J]. BMC Plant Biology, 2019, 19: 1–19.
[36] Thode V A, Lohmann L G. Comparative chloroplast genomics at low taxonomic levels: a case study using Amphilophium (Bignonieae, Bignoniaceae) [J]. Frontiers in Plant Science, 2019, 10: 796.
[37] Rokas A, Williams B L, King N, Carroll S B. Genome-scale approaches to resolving incongruence in molecular phylogenies [J]. Nature, 2003, 425(6960): 798–804.
Outlines

/