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The Soursop Genome (Annona muricata L., Annonaceae)

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Underutilised Crop Genomes

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

The Annonaceae family contains important tropical crops, but the number of species used commercially is limited, and development of other promising species for cultivation is hindered by a lack of genomic resources to support the building of breeding programmes. The family is part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide novel resources to both plant breeders and evolutionary research, we described the chromosome-level genome assembly of the soursop (Annona muricata L.), using DNA data generated with PacBio and Illumina short-read technology, in combination with 10XGenomics, BioNano data, and Hi-C sequencing. To disentangle key angiosperm relationships, we reconstructed phylogenomic trees comparing a wider sampling of available angiosperm genomes and reveal that the soursop represents a genomic mosaic supporting different evolutionary histories, with scaffolds almost exclusively supporting singular topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previously published whole genome-based studies remained inconclusive. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history. The soursop is the first genome assembled in Annonaceae and supports further studies of floral evolution in magnoliids, whilst providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement in promising Annonaceae fruit crops and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource will further strengthen the role of Annonaceae as a model group for research on the ecology, evolution, and domestication potential of tropical species in pomology and agroforestry.

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References

  • Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J (2014) In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res 24(12):2041–2049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amborella Genome Project (2013) The Amborella genome and the evolution of flowering plants. Science 342(6165):1241089

    Article  Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aniama SO, Usman SS, Ayodele SM (2016) Ethnobotanical documentation of some plants among Igala people of Kogi State. Int J Eng Sci 5(4):33–42

    Google Scholar 

  • Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–796

    Article  Google Scholar 

  • Arimoto A, Nishitsuji K, Higa Y, Arakaki N, Hisata K, Shinzato C, Satoh N, Shoguchi E (2019) A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants. DNA Res 26(2):183–192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Artika IM, Julistiono H, Bermawie N, Riyanti EI, Hasan AE (2017) Anticancer activity test of ethyl acetate extract of endophytic fungi isolated from soursop leaf (Annona muricata L.). Asian Pacific J Trop Med 10(6):566–571.

    Google Scholar 

  • Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Valè G, Cattivelli L (2016) Next generation breeding. Plant Sci 242:3–13

    Article  CAS  PubMed  Google Scholar 

  • Barlow J, França F, Gardner TA, Hicks CC, Lennox GD, Berenguer E, Castello L, Economo EP, Ferreira J, Guénard B, Leal CG (2018) The future of hyperdiverse tropical ecosystems. Nature 559(7715):517–526

    Article  CAS  PubMed  Google Scholar 

  • Bell CD, Soltis DE, Soltis PS (2010) The age and diversification of the angiosperms re-revisited. Am J Bot 97:1296–1303

    Article  PubMed  Google Scholar 

  • Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’Donovan C, Phan I, Pilbout S (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31(1):365–370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinform 10(1):421

    Article  Google Scholar 

  • Castresana J (2002) Gblocks, v.0.91b. Online version available at http://molevol.cmima.csic.es/castresana.Gblocks_server.html

  • Chatrou LW, Pirie MD, Erkens RH, Couvreur TL, Neubig KM, Abbott JR, Mols JB, Maas JW, Saunders RM, Chase MW (2012) A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics. Botanical J Linnean Soc 1;169(1):5–40

    Google Scholar 

  • Chaw SM, Liu YC, Wu YW, Wang HY, Lin CY, Wu CS, Ke HM, Chang LY, Hsu CY, Yang HT, Sudianto E (2019) Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nat Plants 5(1):63–73

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen J, Hao Z, Guang X, Zhao C, Wang P, Xue L, Zhu Q, Yang L, Sheng Y, Zhou Y, Xu H (2019) Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation. Nat Plants 5(1):18–25

    Article  CAS  PubMed  Google Scholar 

  • Collevatti RG, Telles MPC, Lima JS, Gouveia FO, Soares TN (2014) Contrasting spatial genetic structure in Annona crassiflora populations from fragmented and pristine savannas. Plant Syst Evol 300:1719–1727

    Article  Google Scholar 

  • Couvreur TL, Helmstetter AJ, Koenen EJ, Bethune K, Brandão RD, Little SA, Sauquet H, Erkens RH (2019) Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes. Front Plant Sci 9:1941

    Article  PubMed  PubMed Central  Google Scholar 

  • De Bie T, Cristianini N, Demuth JP, Hahn MW (2006) CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22:1269–1271

    Article  PubMed  Google Scholar 

  • Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321

    Article  CAS  PubMed  Google Scholar 

  • Dongen SV (2000) Graph clustering by flow simulation. Ph.D. thesis, University of Utrecht

    Google Scholar 

  • Doyle JA, Le Thomas A (1994) Cladistic analysis and pollen evolution in Annonaceae. Acta Botanica Gallica 141(2):149–170

    Article  Google Scholar 

  • Doyle JA, Le Thomas A (1996) Phylogenetic analysis and character evolution in Annonaceae. Adansonia 18:279–334

    Google Scholar 

  • Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 5(1):113

    Article  Google Scholar 

  • Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1–19

    Article  CAS  PubMed  Google Scholar 

  • Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, Glenn TC, Zhong B, Wu S, Lemmon EM, Lemmon AR, Leaché AD (2016) Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Mol Phylogenet Evol 94:447–462

    Article  PubMed  Google Scholar 

  • El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer EL (2019) The Pfam protein families database in 2019. Nucleic Acids Res 47(D1):D427–D432

    Article  CAS  PubMed  Google Scholar 

  • English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA (2012) Mind the gap: upgrading genomes with pacific biosciences RS long-read sequencing technology. PLoS ONE 7:e47768–e47768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS (1998) Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci 95:4441–4446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29–W37

    Google Scholar 

  • Foster CSP, Sauquet H, Van Der Merwe M, McPherson H, Rossetto M, Ho SYW (2016) Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale. Syst Biol 66:338–351

    Google Scholar 

  • Freitas L, Mello B, Schrago CG (2018) Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda. J Evol Biol 31:1623–1631

    Article  PubMed  Google Scholar 

  • Gavamukulya Y, Wamunyokoli F, El-Shemy HA (2017) Annona muricata: is the natural therapy to most disease conditions including cancer growing in our backyard? A systematic review of its research history and future prospects. Asian Pac J Trop Med 10(9):835–848

    Article  PubMed  Google Scholar 

  • Gentry AH (1993) Four neotropical rainforests. Yale University Press, New Haven

    Google Scholar 

  • Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci 108(4):1513–1518

    Article  CAS  PubMed  Google Scholar 

  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321

    Article  CAS  PubMed  Google Scholar 

  • Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to assemble spliced alignments. Genome Biol 9(1):R7

    Article  PubMed  PubMed Central  Google Scholar 

  • Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37(suppl_1):D211–D215

    Google Scholar 

  • IUCN (2020) “Annonaceae”. The IUCN Red List of Threatened Species. Version 2020-2. https://www.iucnredlist.org. Accessed on 7 Sept 2020

  • Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 12;346(6215):1320–1331

    Google Scholar 

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36–R36

    Article  PubMed  PubMed Central  Google Scholar 

  • Koek‐Noorman J, Westra LT, Maas PJ (1990) Studies in Annonaceae. XIII. The role of morphological characters in subsequent classifications of Annonaceae: a comparative survey. Taxon 39(1):16–32

    Google Scholar 

  • Kohlhase M (2006) CodeML: an open markup format the content and presentation of program code. Available from: https://svn.omdoc.org/repos/codeml/doc/spec/codeml

  • Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639–1645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu N, Yang HL, Wang P, Lu YC, Yang YJ, Wang L, Lee SC (2016) Functional proteomic analysis revels that the ethanol extract of Annona muricata L. induces liver cancer cell apoptosis through endoplasmic reticulum stress pathway. J Ethnopharmacol 189:210–217

    Article  PubMed  Google Scholar 

  • Liu S, Hansen MM (2017) PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data. Mol Ecol Resour 17:631–641

    Article  CAS  PubMed  Google Scholar 

  • Lowe TM, Eddy SR (1996) TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1(1):2047–2117

    Article  Google Scholar 

  • Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M (2008a) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 148(4):1772–1781

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lyons E, Pedersen B, Kane J, Freeling M (2008b) The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Tropical Plant Biology 1(3–4):181–190

    Article  CAS  Google Scholar 

  • Massoni J, Couvreur TLP, Sauquet H (2015) Five major shifts of diversification through the long evolutionary history of Magnoliidae (angiosperms). BMC Evol Biol 15:1–14

    Article  Google Scholar 

  • Massoni J, Forest F, Sauquet H (2014) Increased sampling of both genes and taxa improves resolution of phylogenetic relationships within Magnoliidae, a large and early-diverging clade of angiosperms. Mol Phylogenet Evol 70:84–93

    Article  PubMed  Google Scholar 

  • Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD (2018) PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res 47:D419–D426

    Article  PubMed Central  Google Scholar 

  • Moore MJ, Hassan N, Gitzendanner MA, Bruenn RA, Croley M, Vandeventer A, Horn JW, Dhingra A, Brockington SF, Latvis M, Ramdial J (2011) Phylogenetic analysis of the plastid inverted repeat for 244 species: insights into deeper-level angiosperm relationships from a long, slowly evolving sequence region. Int J Plant Sci 172(4):541–558

    Article  Google Scholar 

  • Moore MJ, Soltis DE, Burleigh JG, Bell CD, Soltis PS, Bell CD, Burleigh JG, Soltis DE (2010) Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci 107:4623–4628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murat F, Armero A, Pont C, Klopp C, Salse J (2017) Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet 49:490

    Article  CAS  PubMed  Google Scholar 

  • Najmuddin SU, Romli MF, Hamid M, Alitheen NB, Abd Rahman NM (2016) Anti-cancer effect of Annona muricata L. leaves crude extract (AMCE) on breast cancer cell line. BMC Complement Alternative Med 16(1):311

    Google Scholar 

  • Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD (2015) Rfam 12.0: updates to the RNA family database. Nucleic Acids Res 43(D1):D130–D137

    Google Scholar 

  • Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933–2935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nickrent DL, Soltis DE (2006) A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Ann Mo Bot Gard 82:208

    Article  Google Scholar 

  • Oliver KR, McComb JA, Greene WK (2013) Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol 5:1886–1901

    Article  PubMed  PubMed Central  Google Scholar 

  • Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067

    Article  CAS  PubMed  Google Scholar 

  • Pirie MD, Chatrou LW, Mols JB, Erkens RH, Oosterhof J (2006) ‘Andean-centred’ genera in the short-branch clade of Annonaceae: testing biogeographical hypotheses using phylogeny reconstruction and molecular dating. J Biogeogr 33(1):31–46

    Article  Google Scholar 

  • Pinto AD, Cordeiro MC, De Andrade SR, Ferreira FR, Filgueiras HD, Alves RE, Kinpara DI (2005) Annona species. International Centre for Underutilised Crops, University of Southampton, Southampton, UK

    Google Scholar 

  • Popenoe W (1919) Batido and other Guatemalan beverages prepared from cacao. Am Anthropol 21(4):403–409

    Article  Google Scholar 

  • Price MN, Dehal PS, Arkin AP (2009) Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Punyasena SW, Eshel G, McElwain JC (2008) The influence of climate on the spatial patterning of Neotropical plant families. J Biogeogr 35:117–130

    Google Scholar 

  • Qiu YL, Li L, Wang B, Xue JY, Hendry TA, Li RQ, Brown JW, Liu Y, Hudson GT, Chen ZD (2010) Angiosperm phylogeny inferred from sequences of four mitochondrial genes. J Syst Evol 43:391–425

    Article  Google Scholar 

  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33(suppl_2):W116–W120.

    Google Scholar 

  • R Development Core Team (2010) R: a language and environment for statistical computing. Available from: http://www.r-project.org

  • Rainer H, Chatrou LW (2014) AnnonBase: World species list of Annonaceae. Available from: https://www.catalogueoflife.org/col/details/database/id/40

  • Ramírez-Barahona S, Sauquet H, Magallón S (2020) The delayed and geographically heterogeneous diversification of flowering plant families. Nat Ecol Evol 4:1232–1238

    Article  PubMed  Google Scholar 

  • Richardson JE, Chatrou LW, Mols JB, Erkens RH, Pirie MD (2004) Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae. Philos Trans R Soc Lond Ser B: Biol Sci 359(1450):1495–1508.

    Google Scholar 

  • Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG (2014) From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol 14:23

    Article  PubMed  PubMed Central  Google Scholar 

  • Sauquet H, von Balthazar M, Magallón S, Doyle JA, Endress PK, Bailes EJ, de Morais EB, Bull-Hereñu K, Carrive L, Chartier M, Chomicki G (2017) The ancestral flower of angiosperms and its early diversification. Nat Commun 8(1):1–10

    Article  Google Scholar 

  • Shaw TI, Ruan Z, Glenn TC, Liu L (2013) STRAW: species TRee analysis web server. Nucleic Acids Res 41:W238–W241

    Article  PubMed  PubMed Central  Google Scholar 

  • Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  PubMed  Google Scholar 

  • Smit A, Hubley R, Green P (2017) RepeatMasker Open-4.0.6. Available from: http://www.repeatmasker.org

  • Smit AF, Hubley R (2008) RepeatModeler Open-1.0. Available from: http://www.repeatmasker.org

  • Smith SA, O’Meara BC (2012) TreePL: Divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28:2689–2690

    Article  CAS  PubMed  Google Scholar 

  • Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, Refulio-Rodriguez NF, Walker JB, Moore MJ, Carlsward BS, Bell CD (2011) Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot 98(4):704–730

    Article  PubMed  Google Scholar 

  • Soltis DE, Soltis PS (2019) Nuclear genomes of two magnoliids. Nat Plants 5:6–6

    Article  PubMed  Google Scholar 

  • Song S, Liu L, Edwards SV, Wu S (2012) Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci 109:14942–14947

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sonké B, Couvreur T (2014) Tree diversity of the Dja Faunal Reserve, southeastern Cameroon. Biodiversity Data J 2

    Google Scholar 

  • Strijk JS, Hinsinger DD, Zhang F, Cao K (2019a) Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research. GigaScience 8(11):giz136

    Google Scholar 

  • Strijk JS, Hinsinger DD, Roeder MM, Chatrou LW, Couvreur TL, Erkens RH, Sauquet H, Pirie MD, Thomas DC, Cao K (2019b) The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence. BioRxiv 1:639153. https://doi.org/10.1101/639153

    Article  CAS  Google Scholar 

  • Strijk JS, Hinsinger DD, Roeder MM, Chatrou LW, Couvreur TL, Erkens RH, Sauquet H, Pirie MD, Thomas DC, Cao K (2021) Chromosome-level reference genome of the soursop (Annona muricata), a new resource for Magnoliid research and tropical pomology. Mol Ecol Resour. https://doi.org/10.22541/au.159103606.66673541

  • Tank DC, Eastman JM, Pennell MW, Soltis PS, Soltis DE, Hinchliff CE, Brown JW, Sessa EB, Harmon LJ (2015) Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. New Phytol 207:454–467

    Article  PubMed  Google Scholar 

  • Tchouto MGP, Yemefack M, De Boer WF, De Wilde JJFE, Van Der Maesen LJG, Cleef AM (2006) Biodiversity hotspots and conservation priorities in the Campo-Ma’an rain forests, Cameroon. Biodiversity Conservation 15:1219–1252

    Article  Google Scholar 

  • Tiley GP, Barker MS, Burleigh JG (2018) Assessing the performance of Ks plots for detecting ancient whole genome duplications. Genome Biol Evol 10(11):2882–2898

    PubMed  PubMed Central  Google Scholar 

  • Toussirot M, Nowik W, Hnawia E, Lebouvier N, Hay AE, De la Sayette A, Dijoux-Franca MG, Cardon D, Nour M (2014) Dyeing properties, coloring compounds and antioxidant activity of Hubera nitidissima (Dunal) Chaowasku (Annonaceae). Dyes Pigm 102:278–284

    Article  CAS  Google Scholar 

  • Vamosi JC, Magallón S, Mayrose I, Otto SP, Sauquet H (2018) Macroevolutionary patterns of flowering plant speciation and extinction. Annu Rev Plant Biol 69:685–706

    Article  CAS  PubMed  Google Scholar 

  • Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y, She G, Sun J (2018) Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci 115(18):E4151–E4158.

    Google Scholar 

  • Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR (2014) Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natil Acad Sci 11;111(45):E4859–E4868

    Google Scholar 

  • Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    Article  CAS  PubMed  Google Scholar 

  • Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:983–983

    Article  CAS  PubMed  Google Scholar 

  • Zeng L, Zhang Q, Sun R, Kong H, Zhang N, Ma H (2014) Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun 5:4956

    Article  CAS  PubMed  Google Scholar 

  • Zhang C, Rabiee M, Sayyari E, Mirarab S (2018) ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform 19:153

    Article  Google Scholar 

  • Zhang N, Zeng L, Shan H, Ma H (2012) Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms. New Phytol 195:923–937

    Article  CAS  PubMed  Google Scholar 

  • Zhang T, Qiao Q, Novikova PY, Wang Q, Yue J, Guan Y, Ming S, Liu T, De J, Liu Y, Al-Shehbaz IA (2019) Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude. Proc Natl Acad Sci 116(14):7137–7146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu Q, Zheng X, Luo J, Gaut BS, Ge S (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–888

    Article  CAS  PubMed  Google Scholar 

  • Zwaenepoel A, Van de Peer Y (2019) wgd—simple command line tools for the analysis of ancient whole-genome duplications. Bioinformatics 1;35(12):2153–2155

    Google Scholar 

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Acknowledgements

Genome sequencing, assembly, and annotation were conducted by the Novogene Bioinformatics Institute. We are grateful to Ghent University Botanical Garden for granting access to their living collections.

Author information

Authors and Affiliations

  1. Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Lao PDR

    Joeri S. Strijk & Damien D. Hinsinger

  2. Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Brunei Darussalam

    Joeri S. Strijk

  3. Xishuangbanna Tropical Botanical Garden (CAS), Menglun, China

    Mareike M. Roeder

  4. Aueninstitut, Institute for Geography and Geoecology, Karlsruhe Institute of Technology, Rastatt, Germany

    Mareike M. Roeder

  5. Systematic and Evolutionary Botany lab, Ghent University, Ghent, Belgium

    Lars W. Chatrou

  6. IRD, DIADE, University Montpellier, Montpellier, France

    Thomas L. P. Couvreur

  7. Maastricht Science Program, Maastricht University, Maastricht, The Netherlands

    Roy H. J. Erkens

  8. National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia

    Hervé Sauquet

  9. Department of Natural History, University Museum, University of Bergen, Bergen, Norway

    Michael D. Pirie

  10. National Parks Board, Singapore Botanic Gardens, Singapore, Singapore

    Daniel C. Thomas

  11. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China

    Kunfang Cao

Authors
  1. Joeri S. Strijk
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  2. Damien D. Hinsinger
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  3. Mareike M. Roeder
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  4. Lars W. Chatrou
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  5. Thomas L. P. Couvreur
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  6. Roy H. J. Erkens
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  7. Hervé Sauquet
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  8. Michael D. Pirie
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  9. Daniel C. Thomas
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  10. Kunfang Cao
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Corresponding author

Correspondence to Joeri S. Strijk .

Editor information

Editors and Affiliations

  1. Biological Sciences, University of Southampton, Southampton, UK

    Mark A. Chapman

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Strijk, J.S. et al. (2022). The Soursop Genome (Annona muricata L., Annonaceae). In: Chapman, M.A. (eds) Underutilised Crop Genomes . Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-031-00848-1_9

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