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Piece and parcel of gymnosperm organellar genomes

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Abstract

Main conclusion

Significant past, present, and potential future research into the organellar (plastid and mitochondrial) genomes of gymnosperms that can provide insight into the unknown origin and evolution of plants is highlighted.

Abstract

Gymnosperms are vascular seed plants that predominated the ancient world before their sister clade, angiosperms, took over during the Late Cretaceous. The divergence of gymnosperms and angiosperms took place around 300 Mya, with the latter evolving into the diverse group of flowering plants that dominate the plant kingdom today. Although gymnosperms have reportedly made some evolutionary innovations, the literature on their genome advances, particularly their organellar (plastid and mitochondrial) genomes, is relatively scattered and fragmented. While organellar genomes can shed light on plant origin and evolution, they are frequently overlooked, due in part to their limited contribution to gene expression and lack of evolutionary dynamics when compared to nuclear genomes. A better understanding of gymnosperm organellar genomes is critical because they reveal genetic changes that have contributed to their unique adaptations and ecological success, potentially aiding in plant survival, enhancement, and biodiversity conservation in the face of climate change. This review reveals significant information and gaps in the existing knowledge base of organellar genomes in gymnosperms, as well as the challenges and research needed to unravel their complexity.

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References

  • Alves A, Cordeiro D, Correia S, Miguel C (2021) Small non-coding RNAs at the crossroads of regulatory pathways controlling somatic embryogenesis in seed plants. Plants 10:504. https://doi.org/10.3390/plants10030504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Archibald John M (2015) Endosymbiosis and eukaryotic cell evolution. Curr Biol 25(19):R911–R921

    CAS  PubMed  Google Scholar 

  • Arimura SI, Ayabe H, Sugaya H et al (2020) Targeted gene disruption of ATP synthases 6–1 and 6–2 in the mitochondrial genome of Arabidopsis thaliana by mitoTALENs. Plant J. https://doi.org/10.1111/tpj.15041

    Article  PubMed  Google Scholar 

  • Avia K, Kärkkäinen K, Lagercrantz U, Savolainen O (2014) Association of FLOWERING LOCUS T/TERMINAL FLOWER 1- like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris). New Phytol 204(1):159–170

    CAS  PubMed  Google Scholar 

  • Birks HJB (2020) Angiosperms versus gymnosperms in the Cretaceous. Proc Natl Acad Sci USA 117(49):30879–30881

    PubMed  PubMed Central  Google Scholar 

  • Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ (2022) The origin and early evolution of plants. Trends Plant Sci 28(3):312–329

    PubMed  Google Scholar 

  • Camargo AP, Call L, Roux S et al (2024) IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. Nucleic Acids Res 52:164–173

    Google Scholar 

  • Caradus JR (2023) Perceptions of plant breeding methods—from ‘phenotypic selection’ to ‘genetic modification’ and ‘new breeding technologies’. NZ J Agric Res 1–49. https://doi.org/10.1080/00288233.2023.2187425

  • Casola C, Koralewski TE (2018) Pinaceae show elevated rates of gene turnover that are robust to incomplete gene annotation. Plant J 95(5):862–876

    CAS  Google Scholar 

  • Chaw SM, Shih ACC, Wang D, Wu YW, Liu SM, Chou TY (2008) The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu Sequences, and abundant RNA editing sites. Mol Biol Evol 25(3):603–615

    CAS  PubMed  Google Scholar 

  • Clark JW, Hetherington AJ, Morris JL et al (2023) Evolution of phenotypic disparity in the plant kingdom. Nat Plants 9:1618–1626. https://doi.org/10.1038/s41477-023-01513-x

    Article  PubMed  PubMed Central  Google Scholar 

  • Condamine FL, Silvestro D, Koppelhus EB, Antonelli A (2020) The rise of angiosperms pushed conifers to decline during global cooling. Proc Natl Acad Sci USA 117(46):28867–28875

    CAS  PubMed  PubMed Central  Google Scholar 

  • Daniell H, ** S, Zhu X-G, Gitzendanner MA, Soltis DE, Soltis PS (2021) Green giant—a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. Plant Biotechnol J 19(3):430–447

    CAS  PubMed  PubMed Central  Google Scholar 

  • Davis CC, Schaefer H (2011) Plant evolution: pulses of extinction and speciation in gymnosperm diversity. Curr Biol 21(24):R995–R998

    CAS  PubMed  Google Scholar 

  • de Jesus A, Batista DM, Monteiro EF, Salzman S, Carvalho LM, Santana K, André T (2022) Structural changes and adaptative evolutionary constraints in FLOWERING LOCUS T and TERMINAL FLOWER1-like genes of flowering plants. Front Genet 13:954015

    Google Scholar 

  • De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK (2017) Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. Mol Biol Evol 34(6):1363–1377

    PubMed  Google Scholar 

  • De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I (2020) Functional and morphological evolution in gymnosperms: a portrait of implicated gene families. Evol Appl 13:210–227. https://doi.org/10.1111/eva.12839

    Article  PubMed  Google Scholar 

  • Estravis-Barcala M, Mattera MG, Soliani C, Bellora N, Opgenoorth L, Heer K, Arana MV (2020) Molecular bases of responses to abiotic stress in trees. J Exp Bot 71(13):3765–3779. https://doi.org/10.1093/jxb/erz532

    Article  CAS  PubMed  Google Scholar 

  • Eyster HN, Beckage B (2022) Conifers may ameliorate urban heat waves better than broadleaf trees: evidence from Vancouver, Canada. Atmosphere 13(5):830. https://doi.org/10.3390/atmos13050830

    Article  Google Scholar 

  • Farhat P, Hidalgo O, Robert T, Siljak-Yakovlev S, Leitch IJ, Adams RP, Bou Dagher-Kharrat M (2019) Polyploidy in the conifer genus Juniperus is unexpectedly high. Front Plant Sci 10:676

    PubMed  PubMed Central  Google Scholar 

  • Fritsche S, Rippel Salgado L, Boron AK, Hanning KR, Donaldson LA, Thorlby G (2022) Transcriptional regulation of pine male and female cone initiation and development: key players identified through comparative transcriptomics. Front Genet 13:815093

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gerullis M, Pieruschka R, Fahrner S, Hartl L, Schurr U, Heckelei T (2023) From genes to policy: mission-oriented governance of plant-breeding research and technologies. Front Plant Sci 14:1235175

  • Guo W, Grewe F, Fan W, Young GJ, Knoop V, Palmer JD, Mower JP (2016) Ginkgo and Welwitschia mitogenomes reveal extreme contrasts in gymnosperm mitochondrial evolution. Mol Biol Evol 33(6):1448–1460

    CAS  PubMed  Google Scholar 

  • Guo W, Zhu A, Fan W, Adams RP, Mower JP (2020) Extensive shifts from cis- to trans-splicing of gymnosperm mitochondrial introns. Mol Biol Evol 37(6):1615–1620

    CAS  PubMed  Google Scholar 

  • Guo WY, Serra-Diaz JM, Eiserhardt WL et al (2023) Climate change and land use threaten global hotspots of phylogenetic endemism for trees. Nat Commun 14:6950. https://doi.org/10.1038/s41467-023-42671-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hogg CJ, Ottwell K, Latch P, Rossetto M, Biggs J, Gilbert A (2022) Threatened species initiative: empowering conservation action using genomic resources. Proc Natl Acad Sci USA 119:e2115643118. https://doi.org/10.1073/pnas.2115643118

    Article  PubMed  PubMed Central  Google Scholar 

  • Hong K, Radian Y, Manda T, Xu H, Luo Y (2023) The development of plant genome sequencing technology and its conservation and application in endangered gymnosperms. Plants 12:4006. https://doi.org/10.3390/plants12234006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang J (2013) Horizontal gene transfer in eukaryotes: the weak-link model. BioEssays 35(10):868–875

    CAS  PubMed  PubMed Central  Google Scholar 

  • Huang KY, Kan SL, Shen TT et al (2022) A comprehensive evolutionary study of chloroplast RNA editing in gymnosperms: a novel type of g-to-a RNA editing is common in gymnosperms. Int J Mol Sci 23:10844. https://doi.org/10.3390/ijms231810844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ichinose M, Sugita M (2017) RNA editing and its molecular mechanism in plant organelles. Genes 8(1):5

    Google Scholar 

  • Ickert-Bond SM, Sousa A, Min Y et al (2020) Polyploidy in gymnosperms—insights into the genomic and evolutionary consequences of polyploidy in Ephedra. Mol Phylo Evol 147:106786. https://doi.org/10.1016/j.ympev.2020.106786

    Article  Google Scholar 

  • Jackman SD, Coombe L, Warren RL et al (2020) Complete mitochondrial genome of a gymnosperm, sitka spruce (Picea sitchensis), indicates a complex physical structure. Genome Biol Evol 12(7):1174–1179

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJ, Bohlmann J, Birol I (2016) Organellar genomes of white spruce (Picea glauca): Assembly and annotation. Genome Biol Evol 8(1):29–41.

  • ** WT, Gernandt DS, Wehenkel C et al (2021) Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines. Proc Natl Acad Sci USA 118(20):e2022302118

    CAS  PubMed  PubMed Central  Google Scholar 

  • Johnston IG (2019) Tension and resolution: dynamic, evolving populations of organelle genomes within plant cells. Mol Plant 12(6):764–783

    CAS  PubMed  Google Scholar 

  • Kan SL, Shen TT, Gong P, Ran JH, Wang XQ (2020) The complete mitochondrial genome of taxus Cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome. BMC Evol Biol 20(1):10

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kan SL, Shen TT, Ran JH, Wang XQ (2021) Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome. BMC Biol 19(1):146

  • Kim Y-J, Zhang D (2018) Molecular control of male fertility for crop hybrid breeding. Trends Plant Sci 23(1):53–65

    CAS  PubMed  Google Scholar 

  • Kim Y-K, Jo S, Cheon S-H, Hong JR, Kim K-J (2023) Ancient horizontal gene transfers from plastome to mitogenome of a nonphotosynthetic orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae). Int J Mol Sci 24(14):11448

    CAS  PubMed  PubMed Central  Google Scholar 

  • Klintenäs M, Pin PA, Benlloch R, Ingvarsson PK, Nilsson O (2012) Analysis of conifer FLOWERING LOCUS T/TERMINAL FLOWER1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage. New Phytol 196(4):1260–1273

    PubMed  Google Scholar 

  • Kozik A, Rowan BA, Lavelle D, Berke L, Schranz ME, Michelmore RW, Christensen AC (2019) The alternative reality of plant mitochondrial DNA: one ring does not rule them all. PLOS Genet 15(8):e1008373

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kress WJ, Soltis DE, Kersey PJ et al (2022) Green plant genomes: what we know in an era of rapidly expanding opportunities. Proc Natl Acad Sci USA 119(4):e2115640118

    PubMed  PubMed Central  Google Scholar 

  • Krupinska K, Blanco NE, Oetke S, Zottini M (2020) Genome communication in plants mediated by organelle–nucleus-located proteins. Philos Trans R Soc B 375:20190397

    CAS  Google Scholar 

  • Kusnetsov VV (2018) Chloroplasts: structure and expression of the plastid genome. Russ J Plant Physiol 65(4):465–476

    CAS  Google Scholar 

  • Lang BF, Beck N, Prince S, Sarrasin M, Rioux P, Burger G (2023) Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction. Front Plant Sci 14:1222186

    PubMed  PubMed Central  Google Scholar 

  • Lehtonen S, Silvestro D, Nikolaus D et al (2017) Environmentally driven extinction and opportunistic origination explain fern diversification patterns. Sci Rep 7:4831

    PubMed  PubMed Central  Google Scholar 

  • Leitch AR, Leitch IJ (2012) Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol 194:629–646

    CAS  PubMed  Google Scholar 

  • Li S, Chang L, Zhang J (2021) Advancing organelle genome transformation and editing for crop improvement. Plant Commun 2(2):100141

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin D, Coombe L, Jackman SD et al (2019) Complete chloroplast genome sequence of a white spruce (Picea glauca, Genotype WS77111) from Eastern Canada. Microbiol Resour Announc 8(23):00381–19

  • Liu ZX, **ong HY, Li LY, Fei YJ (2018) Functional conservation of an AGAMOUS orthologous gene controlling reproductive organ development in the gymnosperm species Taxus chinensis var. mairei. J Plant Biol 61(1):50–59

    CAS  Google Scholar 

  • Liu HL, Wang XB, Wang GB et al (2021) The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. Nat Plants 7:748–756

    CAS  PubMed  Google Scholar 

  • Liu H, Zhao W, Zhang RG, Mao JF, Wang XR (2022a) Repetitive elements, sequence turnover and cytonuclear gene transfer in gymnosperm mitogenomes. Front Genet 13:867736

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Wang SB, Li LZ et al (2022b) The Cycas genome and the early evolution of seed plants. Nat Plants 8:389–401. https://doi.org/10.1038/s41477-022-01129-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu WZ, Shen HX, Wang X (2023) A novel gymnosperm reproductive organ from the Jurassic of China. Palaeiworld. https://doi.org/10.1016/j.palwor.2023.03.002

    Article  Google Scholar 

  • Lou H, Song L, Li X et al (2023) The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis. Nat Commun 14:1315. https://doi.org/10.1038/s41467-023-37038-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu Y, ** B, Wang L, Wang Y, Wang D, Jiang XX, Chen P (2011) Adaptation of male reproductive structures to wind pollination in gymnosperms: cones and pollen grains. Can J Plant Sci 91:897–906

    Google Scholar 

  • Lubna AS, Khan AL, Jan R, Khan A, Khan A, Kim KM, Lee IJ (2021) The dynamic history of gymnosperm plastomes: insights from structural characterization, comparative analysis, phylogenomics, and time divergence. Plant Genome 14:e20130

    CAS  PubMed  Google Scholar 

  • Lukes J, Kaur B, Speijer D (2021) RNA editing in mitochondria and plastids: weird and widespread. Trends Genet 37:99–102

    CAS  PubMed  Google Scholar 

  • Ma J, Chen X, Han F, Song Y et al (2022) The long road to bloom in conifers. For Res 2:16. https://doi.org/10.48130/FR-2022-0016

    Article  Google Scholar 

  • Mahapatra K, Banerjee S, De S, Mitra M, Roy P, Roy S (2021) An insight into the mechanism of plant organelle genome maintenance and implications of organelle genome in crop improvement: an update. Front Cell Dev Biol 9:671698

    PubMed  PubMed Central  Google Scholar 

  • Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM (2021) BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol 38:4647–4654

    CAS  PubMed  PubMed Central  Google Scholar 

  • Martin W, Herrmann RG (1998) Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol 118(1):9–17

    CAS  PubMed  PubMed Central  Google Scholar 

  • Maul JE, Lilly JW, Cui L et al (2002) The Chlamydomonas reinhardtii plastid chromosome: Islands of genes in a sea of repeats. Plant Cell 14(11):2659–2679

    CAS  PubMed  PubMed Central  Google Scholar 

  • McCoy SR, Kuehl JV, Boore JL, Raubeson LA (2008) The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol 8(1):130

    PubMed  PubMed Central  Google Scholar 

  • Mohanta TK, Mishra AK, Khan A, Hashem A, Abd Allah EF, Al-Harrasi A (2020) Gene loss and evolution of the plastome. Genes 11(10):1133

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA 104(49):19363–19368

    PubMed  PubMed Central  Google Scholar 

  • Morley SA, Ahmad N, Nielsen BL (2019) Plant organelle genome replication. Plants 8(10):358

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mower JP, Touzet P, Gummow JS et al (2007) Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7:135

    PubMed  PubMed Central  Google Scholar 

  • Mower JP, Sloan DB, Alverson AJ (2012) Plant mitochondrial genome diversity: the genomics revolution. In: Wendel JF, Greilhuber J, Dolezel J, Leitch IJ (eds) Plant genome diversity volume 1: plant genomes, their residents, and their evolutionary dynamics. Springer Vienna, Vienna, pp 123–144

    Google Scholar 

  • Moyroud E, Monniaux M, Thévenon E, Dumas R, Scutt CP, Frohlich MW, Parcy F (2017) A link between LEAFY and B-gene homologues in Welwitschia mirabilis sheds light on ancestral mechanisms prefiguring floral development. New Phytol 216(2):469–481

    CAS  PubMed  Google Scholar 

  • Neale DB, Zimin AV, Zaman S et al (2022) Assembled and annotated 26.5 gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3. https://doi.org/10.1093/g3journal/jkab380

    Article  PubMed  Google Scholar 

  • Niu SH, Liu C, Yuan HW, Li P, Li Y, Li W (2015) Identification and expression profiles of sRNAs and their biogenesis and action-related genes in male and female cones of Pinus tabuliformis. BMC Genom 16(1):693

    Google Scholar 

  • Niu SH, Yuan HW, Sun X, Porth I, Li Y, El-Kassaby YA, Li W (2016) A transcriptomics investigation into pine reproductive organ development. New Phytol 209:1278–1289

    CAS  PubMed  Google Scholar 

  • Niu SH, Li J, Bo WH et al (2022) The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 185:204–217. https://doi.org/10.1016/j.cell.2021.12.006

    Article  CAS  PubMed  Google Scholar 

  • Offer E, Moschin S, Nigris S, Baldan B (2023) Reproductive mechanisms in ginkgo and cycas: sisters but not twins. Crit Rev Plant Sci 42(5):283–299

    Google Scholar 

  • Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ (2018) Genome size diversity and its impact on the evolution of land plants. Genes 9(2):88

    PubMed  PubMed Central  Google Scholar 

  • Pennisi E (2009) On the origin of flowering plants. Science 324(5923):28–31

    CAS  PubMed  Google Scholar 

  • Petterle A, Karlberg A, Bhalerao RP (2013) Daylength mediated control of seasonal growth patterns in perennial trees. Curr Opin Plant Biol 16(3):301–306

    PubMed  Google Scholar 

  • Putintseva YA, Bondar EI, Simonov EP et al (2020) Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome. BMC Genom 21:654

    Google Scholar 

  • Qi Y, Liu H, Xu C, Dai J, Han B (2023) Dry climate filters gymnosperms but not angiosperms through seed mass. Diversity 15(3):401. https://doi.org/10.3390/d15030401

    Article  Google Scholar 

  • Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW, Knox EB, Palmer JD (2013) Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 342(6165):1468–1473

    CAS  PubMed  Google Scholar 

  • Robles P, Quesada V (2021) Organelle genetics in plants. Int J Mol Sci 22(4):2104

    PubMed  PubMed Central  Google Scholar 

  • Rodrigues AS, Miguel CM (2017) The pivotal role of small non-coding RNAs in the regulation of seed development. Plant Cell Rep 36(5):653–667

    CAS  PubMed  Google Scholar 

  • Rodrigues AS, De Vega JJ, Miguel CM (2018) Comprehensive assembly and analysis of the transcriptome of maritime pine develo** embryos. BMC Plant Biol 18:379

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sakamoto W, Takami T (2018) Chloroplast DNA dynamics: copy number, quality control and degradation. Plant Cell Physiol 59(6):1120–1127

    CAS  PubMed  Google Scholar 

  • Scheneider H (2023) Integrating genomics and conservation to safeguard plant diversity. Intergrative Conserv 2(1):10–18

    Google Scholar 

  • Sharma P, Jha AB, Dubey RS, Pessarakli M (2012) Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. J Bot. https://doi.org/10.1155/2012/217037

    Article  Google Scholar 

  • Singh S, Naik J, Pandey A (2022) Genetics of plant organelles: plastid and mitochondrial genomes. In: Singh RL, Mondal S, Parihar A, Singh PK (eds) Plant genomics for sustainable agriculture. Springer Nature Singapore, Singapore, pp 313–330

    Google Scholar 

  • Siqueira JA, Hardoim P, Ferreira PCG, Nunes-Nesi A, Hemerly AS (2018) Unraveling interfaces between energy metabolism and cell cycle in plants. Trends Plant Sci 23(8):731–747

    CAS  PubMed  Google Scholar 

  • Šmarda P, Bureš P (2012) The variation of base composition in plant genomes. In: Wendel JF, Greilhuber J, Dolezel J, Leitch IJ (eds) Plant genome diversity volume 1: plant genomes, their residents, and their evolutionary dynamics. Springer Vienna, Vienna, pp 209–235

    Google Scholar 

  • Smith DR, Keeling PJ (2015) Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci USA 112(33):10177–10184

    CAS  PubMed  PubMed Central  Google Scholar 

  • Son S, Park SR (2022) Challenges facing CRISPR/Cas9-based genome editing in plants. Front Plant Sci 13:902413

    PubMed  PubMed Central  Google Scholar 

  • Stephan T, Burgess SM, Cheng H, Danko CG et al (2022) Darwinian genomics and diversity in the tree of life. Proc Natl Acad Sci USA 119(4):e2115644119

  • Sullivan AR, Eldfjell Y, Schiffthaler B et al (2020) The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants. Genome Biol Evol 12(1):3586–3598

    CAS  PubMed  Google Scholar 

  • Tyszka AS, Bretz EC, Robertson HM, Woodcock-Girard MD, Ramanauskas K, Larson DA, Stull GW, Walker JF (2023) Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. Front Plant Sci 14:1125107

    PubMed  PubMed Central  Google Scholar 

  • Umair M, Hu X, Cheng Q, Ali S, Ni J (2023) Distribution patterns of gymnosperm species along elevations on the Qinghai-Tibet plateau: effects of climatic seasonality, energy-water, and physical tolerance variables. Plants 12(23):4066

    PubMed  PubMed Central  Google Scholar 

  • Valderrama-Martín JM, Ortigosa F, Cantón FR et al (2023) Emerging insights into nitrogen assimilation in gymnosperms. Trees. https://doi.org/10.1007/s00468-023-02403-7

    Article  Google Scholar 

  • Van Aken O, Van Breusegem F (2015) Licensed to kill: mitochondria, chloroplasts, and cell death. Trends Plant Sci 20(11):754–766

    PubMed  Google Scholar 

  • Van Dingenen J, Blomme J, Gonzalez N, Inzé D (2016) Plants grow with a little help from their organelle friends. J Exp Bot 67(22):6267–6281

    PubMed  Google Scholar 

  • Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M (1994) Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA 91(21):9794–9798

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wan T, Gong Y, Liu Z, Zhou Y, Dai C, Wang Q (2022) Evolution of complex genome architecture in gymnosperms. GigaSci. https://doi.org/10.1093/gigascience/giac078

    Article  Google Scholar 

  • Wang X (2023) Origin of angiosperms: problems, challenges, and solutions. Life 13:2029. https://doi.org/10.3390/life13102029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang D, Wu Y-W, Shih AC-C, Wu C-S, Wang Y-N, Chaw S-M (2007) Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 Mya. Mol Biol Evol 24(9):2040–2048

    CAS  PubMed  Google Scholar 

  • Wang J, Kan S, Liao X et al (2024) Plant organellar genomes: much done, much more to do. Trends Plant Sci. https://doi.org/10.1016/j.tplants.2023.12.014

    Article  PubMed  Google Scholar 

  • Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76(3):273–297

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu ZQ, Waneka G, Broz AK, King CR, Sloan DB (2020) MSH1 is required for the maintenance of the low mutation rates in plant mitochondrial and plastid genomes. Proc Natl Acad Sci USA 117:16448–16455

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu ZQ, Liao XZ, Zhang XN, Tembrock LR, Broz A (2022) Genomic architectural variation of plant mitochondria—a review of multichromosomal structuring. J Syst Evol 60(1):160–168

    Google Scholar 

  • **a C, Li J, Zuo Y, He P, Zhang H, Zhang X, Wang B, Zhang J, Yu J, Weng H (2023) Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae. BMC Plant Biol 23:84

  • **ao-Ming Z, Junrui W, Li F et al (2017) Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. Sci Rep 7(1):1555

    PubMed  PubMed Central  Google Scholar 

  • Yang X, Zhou T, Su X, Wang G, Zhang X, Guo Q, Cao F (2021) Structural characterization and comparative analysis of the chloroplast genome of Ginkgo biloba and other gymnosperms. J Forest Res 32(2):765–778

    CAS  Google Scholar 

  • Yang Y, Ferguson DK, Liu B, Mao KS, Gao LM, Zhang SZ, Wan T, Rushforth K, Zhang ZX (2022) Recent advances on phylogenomics of gymnosperms and a new classification. Plant Divers 44(4):340–350

    PubMed  PubMed Central  Google Scholar 

  • Yeoh XH-Y, Durodola B, Blumenstein K, Terhonen E (2021) Drought stress described by transcriptional responses of Picea abies (L.) H. Karst. under pathogen Heterobasidion parviporum attack. Forests 12(10):1379

    Google Scholar 

  • Yu X, Wei P, Chen Z et al (2023) Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences. BMC Plant Biol 23:156. https://doi.org/10.1186/s12870-023-04159-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang M, Zheng CX (2016) Archegonium and fertilization in Coniferopsida. Trees 30:75–86

    CAS  Google Scholar 

  • Zhou W, Armijos CE, Lee C, Lu R, Wang J, Ruhlman TA, Jansen RK, Jones AM, Jones CD (2023) Plastid genome assembly using long-read data. Mol Ecol Resour 2(6):1442–1457

    Google Scholar 

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Acknowledgements

This work was supported by the SATU Joint Research Scheme [Grant Number: ST011-2022] and Universiti Malaya Research Excellence Grant [Grant Number: UMREG026-2023]. We would like to thank Dr. Edi Sudianto for hel** to design the structure of the review.

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Conceptualization: Acga Cheng and Najiah Mohd. Sadali; Writing—original draft preparation: Acga Cheng, Najiah Mohd. Sadali and Nur Ardiyana Rejab; Writing—review and editing: Acga Cheng and Najiah Mohd. Sadali, Nur Ardiyana Rejab and Ahmet Uludag; Funding acquisition: Acga Cheng.

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Correspondence to Acga Cheng.

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Cheng, A., Sadali, N.M., Rejab, N.A. et al. Piece and parcel of gymnosperm organellar genomes. Planta 260, 14 (2024). https://doi.org/10.1007/s00425-024-04449-4

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