Berg CC. Classification and distribution of Ficus. Experientia. 1989;45(7):605–11. https://doi.org/10.1007/BF01975677.
Article
Google Scholar
Berg CC, Corner EJH. Moraceae (Ficus). Flora malesiana. series I, volume 17. Nooteboom HP. eds. National herbarium Nederland, Universiteit Leiden branch, The Netherlands. 2005:1–702.
Seraia AS, Tsybulia NV, Dul’tseva GG. Role of some species of Ficus in amelioration of environment. Aviakosm Ekolog Med. 2008;42(4):66–70 (PMID: 19140478).
CAS
PubMed
Google Scholar
Harrison R. Figs and the diversity of tropical rainforests. Bioscience. 2009;55:1053–64. https://doi.org/10.1641/0006-3568(2005)055[1053:FATDOT]2.0.CO;2.
Article
Google Scholar
Barolo MI, Ruiz Mostacero N, López SN. Ficus carica L. (Moraceae): An ancient source of food and health. Food Chemistry. 2014;164:119–27. https://doi.org/10.1016/j.foodchem.2014.04.112.
Article
CAS
PubMed
Google Scholar
Dangarembizi R, Erlwanger KH, Moyo D, Chivandi E. Phytochemistry, pharmacology and ethnomedicinal uses of Ficus thonningii (Blume Moraceae): a review. Afr J Tradit Complement Altern Med. 2012;10(2):203–12. https://doi.org/10.4314/ajtcam.v10i2.4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ayoub L, Hassan F, Hamid S, Abdelhamid Z, Souad A. Phytochemical screening, antioxidant activity and inhibitory potential of Ficus carica and Olea europaea leaves. Bioinformation. 2019;15(3):226–32. https://doi.org/10.6026/97320630015226.
Article
PubMed
PubMed Central
Google Scholar
Villard C, Larbat R, Munakata R, Hehn A. Defence mechanisms of Ficus: pyramiding strategies to cope with pests and pathogens. Planta. 2019;249(3):617–33. https://doi.org/10.1007/s00425-019-03098-2.
Article
CAS
PubMed
Google Scholar
Lansky EP, Paavilainen HM, Pawlus AD, Newman RA. Ficus spp. (fig): Ethnobotany and potential as anticancer and anti-inflammatory agents. J Ethnopharmacol. 2008;119(2):195–213. https://doi.org/10.1016/j.jep.2008.06.025.
Article
CAS
PubMed
Google Scholar
Yao J, Wang Z, Wang R, Wang Y, Xu J, He X. Anti-proliferative and anti-inflammatory prenylated isoflavones and coumaronochromones from the fruits of Ficus altissima. Bioorg Chem. 2021;113:104996–5016. https://doi.org/10.1016/j.bioorg.2021.104996.
Article
CAS
PubMed
Google Scholar
Pandit R, Phadke A, Jagtap A. Antidiabetic effect of Ficus religiosa extract in streptozotocin-induced diabetic rats. J Ethnopharmacol. 2010;128(2):462–6. https://doi.org/10.1016/j.jep.2010.01.025.
Article
PubMed
Google Scholar
El-Mostafa K, El Kharrassi Y, Badreddine A, Andreoletti P, Vamecq J, El Kebbaj M, et al. Nopal Cactus (Opuntia ficus-indica) as a Source of Bioactive Compounds for Nutrition, Health and Disease. Molecules. 2014;19(9):14879–901. https://doi.org/10.3390/molecules190914879.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pothasin P, Compton SG, Wangpakapattanawong P. Riparian Ficus tree communities: the distribution and abundance of riparian fig trees in northern Thailand. PLoS ONE. 2014;9(10):489–512. https://doi.org/10.1371/journal.pone.0108945.
Article
CAS
Google Scholar
Corner EJH. Check-list of Ficus in Asia and Australasia with keys to identification. The Gardens’ bulletin, Singapore. 1965;21(1):1–186.
Google Scholar
William RB. A New Classification of Ficus. Ann Mo Bot Gard. 1977;64:296–310. https://doi.org/10.2307/2395337.
Article
Google Scholar
Weiblen G. Phylogenetic Relationships of Functionally Dioecious Ficus (Moraceae) Based on Ribosomal DNA Sequences and Morphology. Am J Bot. 2000;87:1342–57. https://doi.org/10.2307/2656726.
Article
CAS
PubMed
Google Scholar
Levy SE, Myers RM. Advancements in Next-Generation Sequencing. Annu Rev Genomics Hum Genet. 2016;17:95–115. https://doi.org/10.1146/annurev-genom-083115-022413.
Article
CAS
PubMed
Google Scholar
Li W, Liu Y, Yang Y, Xie X, Lu Y, Yang Z, et al. Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros. BMC Plant Biol. 2018;18(1):210–23. https://doi.org/10.1186/s12870-018-1421-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feng S, Zheng K, Jiao K, Cai Y, Chen C, Mao Y, et al. Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships. BMC Plant Biol. 2020;20(1):242–68. https://doi.org/10.1186/s12870-020-02429-w.
Article
PubMed
PubMed Central
Google Scholar
Chen Y, Hu N, Wu H. Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii. Biomed Res Int. 2019;2019:5190425. https://doi.org/10.1155/2019/5190425.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nie L, Cui Y, Chen X, Xu Z, Sun W, Wang Y, et al. Complete chloroplast genome sequence of the medicinal plant Arctium lappa. Genome. 2020;63(1):53–60. https://doi.org/10.1139/gen-2019-0070.
Article
CAS
PubMed
Google Scholar
Dong W, Liu J, Yu J, Wang L, Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE. 2012;7(4):e35071. https://doi.org/10.1371/journal.pone.0035071.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu F-H, Chan M-T, Liao D-C, Hsu C-T, Lee Y-W, Daniell H, et al. Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biol. 2010;16(10):68–86. https://doi.org/10.1186/1471-2229-10-68.
Article
CAS
Google Scholar
Zhang Y, Iaffaldano BJ, Zhuang X, Cardina J, Cornish K. Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives. BMC Plant Biol. 2017;17(1):34–45. https://doi.org/10.1186/s12870-016-0967-1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Daniell H, Lin C-S, Yu M, Chang W-J. Chloroplast Genomes: Diversity, Evolution, and Applications in Genetic Engineering. Genome Biol. 2016;17(1):134–45. https://doi.org/10.1186/s13059-016-1004-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kohchi T, Yamato KT, Ishizaki K, Yamaoka S, Nishihama R. Development and Molecular Genetics of Marchantia polymorpha. Annu Rev Plant Biol. 2021;72:677–702. https://doi.org/10.1146/annurev-arplant-082520-094256.
Article
CAS
PubMed
Google Scholar
Chen H, Shao J, Zhang H, Jiang M, Huang L, Zhang Z, et al. Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm. Front Plant Sci. 2018;9:324–38. https://doi.org/10.3389/fpls.2018.00324.
Article
PubMed
PubMed Central
Google Scholar
Huang H, Shi C, Liu Y, Mao S-Y, Gao L-Z. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: Genome structure and phylogenetic relationships. BMC Evol Biol. 2014;14:151–68. https://doi.org/10.1186/1471-2148-14-151.
Article
PubMed
PubMed Central
Google Scholar
Shaul O. How introns enhance gene expression. Int J Biochem Cell Biol. 2017;91:145–55. https://doi.org/10.1016/j.biocel.2017.06.016.
Article
CAS
PubMed
Google Scholar
Qiujie Z, Ng WL, Wu W, Zhou R, Liu Y. Characterization of the complete chloroplast genome sequence of Tigridiopalma magnifica (Melastomataceae). Conserv Genet Resour. 2018;10:571–3. https://doi.org/10.1007/s12686-017-0856-4.
Article
Google Scholar
Bruun-Lund S, Clement WL, Kjellberg F, Rønsted N. First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae). Mol Phylogenet Evol. 2017;109:93–104. https://doi.org/10.1016/j.ympev.2016.12.031.
Article
PubMed
Google Scholar
Zeng Q, Chen H, Zhang C, Han M, Li T, Qi X, et al. Definition of Eight Mulberry Species in the Genus Morus by Internal Transcribed Spacer-Based Phylogeny. PLoS ONE. 2015;10(8):e0135411. https://doi.org/10.1371/journal.pone.0135411.
Article
CAS
PubMed
PubMed Central
Google Scholar
Payacan C, Moncada X, Rojas G, Clarke A, Chung K-F, Allaby R, et al. Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific. Ann Bot. 2017;120(3):387–404. https://doi.org/10.1093/aob/mcx062.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen X, Guo S, Yin Y, Zhang J, Yin X, Liang C, et al. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus. Molecules (Basel, Switzerland). 2018;23(10):2426–38. https://doi.org/10.3390/molecules23102426.
Article
CAS
Google Scholar
Zhang J, Liao M, Li X, Xu B. Characterization and phylogenetic analysis of the complete chloroplast genome sequence of xerophyta retinervis (velloziaceae). Mitochondrial DNA Part B. 2022;7:681–2. https://doi.org/10.1080/23802359.2022.2067500.
Article
PubMed
PubMed Central
Google Scholar
Timme RE, Kuehl JV, Boore JL, Jansen RK. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot. 2007;94(3):302–12. https://doi.org/10.3732/ajb.94.3.302.
Article
CAS
PubMed
Google Scholar
Kim T-S, Booth JG, Gauch HG, Sun Q, Park J, Lee Y-H, et al. Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference. BMC Genomics. 2008;9:31–42. https://doi.org/10.1186/1471-2164-9-31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qi W-H, Jiang X-M, Yan C-C, Zhang W-Q, Xiao G-S, Yue B-S, et al. Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes. Sci Rep. 2018;8(1):14407–16. https://doi.org/10.1038/s41598-018-32286-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim K-J, Lee H-L. Complete Chloroplast Genome Sequences from Korean Ginseng ( Panax schinseng Nees) and Comparative Analysis of Sequence Evolution among 17 Vascular Plants. DNA Res. 2004;11(4):247–61. https://doi.org/10.1093/dnares/11.4.247.
Article
CAS
PubMed
Google Scholar
Kashi Y, King DG. Simple sequence repeats as advantageous mutators in evolution. Trends Genet. 2006;22(5):253–9. https://doi.org/10.1016/j.tig.2006.03.005.
Article
CAS
PubMed
Google Scholar
Srivastava D, Shanker A. Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach. Interdiscip Sci. 2015;8:327–36. https://doi.org/10.1007/s12539-015-0129-4.
Article
PubMed
Google Scholar
Mazumdar P, Othman R, Mebus K, Ramakrishnan N, Harikrishna J. Codon usage and codon pair patterns in non-grass monocot genomes. Ann Bot. 2017;00:1–17. https://doi.org/10.1093/aob/mcx112.
Article
CAS
Google Scholar
Sloan D, Taylor D. Testing for Selection on Synonymous Sites in Plant Mitochondrial DNA: The Role of Codon Bias and RNA Editing. J Mol Evol. 2010;70:479–91. https://doi.org/10.1007/s00239-010-9346-y.
Article
CAS
PubMed
Google Scholar
LaBella A, Opulente D, Steenwyk J, Hittinger C, Rokas A. Variation and selection on codon usage bias across an entire subphylum. PLoS Genet. 2019;15:e1008304. https://doi.org/10.1371/journal.pgen.1008304.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li G, Pan Z, Gao S, He Y, Xia Q, Jin Y, et al. Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis. Genes Genomics. 2019;41(10):1173–81. https://doi.org/10.1007/s13258-019-00847-1.
Article
CAS
PubMed
Google Scholar
He P, Huang S, Xiao G, Zhang Y, Yu J. Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis. BMC Plant Biol. 2016;16(1):257–65. https://doi.org/10.1186/s12870-016-0944-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brenner WG, Mader M, Müller NA, Hoenicka H, Schroeder H, Zorn I, et al. High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species. G3 (Bethesda). 2019;9(3):709–917. https://doi.org/10.1534/g3.118.200763.
Article
CAS
Google Scholar
Kawabe A, Furihata H, Tsujino Y, Kawanabe T, Fujii S, Yoshida T. Divergence of RNA editing among Arabidopsis species. Plant Sci. 2018;280:241–7. https://doi.org/10.1016/j.plantsci.2018.12.009.
Article
CAS
PubMed
Google Scholar
Reginato M, Neubig KM, Majure LC, Michelangeli FA. The first complete plastid genomes of Melastomataceae are highly structurally conserved. PeerJ. 2016;4:e2715. https://doi.org/10.7717/peerj.2715.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang X, Zhou T, Bai G, Zhao Y. Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships. Sci Rep. 2018;8(1):12379–88. https://doi.org/10.1038/s41598-018-30398-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Asaf S, Khan A, Khan A, Waqas M, Kang S-M, Khan M, et al. Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species. Front Plant Sci. 2016;14(7):843–54. https://doi.org/10.3389/fpls.2016.00843.
Article
Google Scholar
Khakhlova O, Bock R. Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J. 2006;46(1):85–94. https://doi.org/10.1111/j.1365-313x.2006.02673.x.
Article
CAS
PubMed
Google Scholar
Liu M-L, Fan W-B, Wang N, Dong P-B, Zhang T-T, Yue M, et al. Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships. Int J Mole Sci. 2018;19:4039–51. https://doi.org/10.3390/ijms19124039.
Article
Google Scholar
Wu Y, Liu F, Yang D-G, Li W, Zhou X-J, Pei X-Y, et al. Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny. Front Plant Sci. 2018;21(9):376–87. https://doi.org/10.3389/fpls.2018.00376.
Article
Google Scholar
Yaradua S, Alzahrani D, Albokhari E, Abba A, Bello A. Complete Chloroplast Genome Sequence of Justicia flava : Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. Biomed Res Int. 2019;2019:1–17. https://doi.org/10.1155/2019/4370258.
Jansen R, Cai Z, Raubeson L, Daniell H, dePamphilis C, Leebens-Mack J, et al. Analysis of 81 Genes From 64 Plastid Genomes Resolves Relationships in Angiosperms and Identifies Genome-Scale Evolutionary Patterns. Proc Natl Acad Sci U S A. 2008;104:19369–74. https://doi.org/10.1073/pnas.0709121104.
Article
Google Scholar
Tuler AC, Carrijo TT, Nóia LR, Ferreira A, Peixoto AL, da Silva Ferreira MF. SSR markers: a tool for species identification in Psidium (Myrtaceae). Mol Biol Rep. 2015;42(11):1501–13. https://doi.org/10.1007/s11033-015-3927-1.
Article
CAS
PubMed
Google Scholar
Yang C-H, Liu X, Cui Y-X, Nie L-P, Lin Y-L, Wei X-P, et al. Molecular structure and phylogenetic analyses of the complete chloroplast genomes of three original species of Pyrrosiae Folium. Chin J Nat Med. 2020;18(8):573–81. https://doi.org/10.1016/S1875-5364(20)30069-8.
Article
CAS
PubMed
Google Scholar
Tang W, Luo C. Molecular and Functional Diversity of RNA Editing in Plant Mitochondria. Mol Biotechnol. 2018;60(12):935–45. https://doi.org/10.1007/s12033-018-0126-z.
Article
CAS
PubMed
Google Scholar
Sasaki T, Yukawa Y, Miyamoto T, Obokata J, Sugiura M. Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing. Mol Biol Evol. 2003;20(7):1028–35. https://doi.org/10.1093/molbev/msg098.
Article
CAS
PubMed
Google Scholar
Zhu A, Guo W, Gupta S, Fan W, Mower J. Evolutionary dynamics of the plastid inverted repeat: The effects of expansion, contraction, and loss on substitution rates. New Phytol. 2015;209(4):1747–56. https://doi.org/10.1111/nph.13743.
Article
CAS
PubMed
Google Scholar
Hebert P, Cywinska A, Ball SL, Dewaard J. Biological identification through DNA barcodes. Proc R Soc London B. 2003;270:313–21. https://doi.org/10.1098/rspb.2002.2218.
Article
CAS
Google Scholar
Cabelin VLD, Alejandro GJD. Efficiency of matK, rbcL, trnH-psbA, and trnL-F (cpDNA) to Molecularly Authenticate Philippine Ethnomedicinal Apocynaceae Through DNA Barcoding. Pharmacogn Mag. 2016;12(3):384–8. https://doi.org/10.4103/0973-1296.185780.
Article
CAS
Google Scholar
Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S, et al. ycf1, the most promising plastid DNA barcode of land plants. Sci Rep. 2015;5:8348–52. https://doi.org/10.1038/srep08348.
Article
CAS
PubMed
PubMed Central
Google Scholar
Roman M, Houston R. Investigation of chloroplast regions rps16 and clpP for determination of Cannabis sativa crop type and biogeographical origin. Leg Med. 2020;47:101759–68. https://doi.org/10.1016/j.legalmed.2020.101759.
Article
CAS
Google Scholar
Yik M, Kong B, Siu TY, Lau D, Cao H, Shaw P-C. Differentiation of Hedyotis diffusa and Common Adulterants Based on Chloroplast Genome Sequencing and DNA Barcoding Markers. Plants. 2021;10:161–72. https://doi.org/10.3390/plants10010161.
Article
CAS
PubMed
PubMed Central
Google Scholar
Awad M, Fahmy RM, Mosa KA, Helmy M, El-Feky FA. Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis. Comput Biol Chem. 2017;71:20–31. https://doi.org/10.1016/j.compbiolchem.2017.09.003.
Article
CAS
PubMed
Google Scholar
Jeon J-H, Kim S-C. Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae). Genes. 2019;10:23–31. https://doi.org/10.3390/genes10010023.
Article
CAS
PubMed Central
Google Scholar
Cheng Y, Yang Y, Fu X, Liu L, Jiang Z, Cai J. Plastid genomes of Elaeagnus mollis: comparative and phylogenetic analyses. J Genet. 2020;99:85–96. https://doi.org/10.1007/s12041-020-01243-5.
Article
PubMed
Google Scholar
Mustapha SB, Ben Tamarzizt H, Baraket G, Abdallah D, Salhi-Hannachi A. Cytoplasmic polymorphism and evolutionary history of plum cultivars: Insights from chloroplast DNA sequence variation of trnL-trnF spacer and aggregated trnL intron & trnL-trnF spacer. Genet Mol Res. 2015;14(2):3964–79. https://doi.org/10.4238/2015.April.27.11.
Article
CAS
PubMed
Google Scholar
Shaw J, Lickey E, Beck J, Farmer S, Liu W, Miller J, et al. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot. 2005;92:142–66. https://doi.org/10.3732/ajb.92.1.142.
Article
CAS
PubMed
Google Scholar
Clement W, Weiblen G. Morphological Evolution in the Mulberry Family (Moraceae). Syst Bot. 2009;34:530–52. https://doi.org/10.1600/036364409789271155.
Article
Google Scholar
Cheon K-S, Yoo K-O. Complete chloroplast genome sequence of Hanabusaya asiatica (Campanulaceae), an endemic genus to Korea. Mitochondrial DNA. 2014;27:1–3. https://doi.org/10.3109/19401736.2014.958702.
Article
CAS
Google Scholar
Raman G, Park S. The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms. Front Plant Sci. 2016;7:341–7. https://doi.org/10.3389/fpls.2016.00341.
Article
PubMed
PubMed Central
Google Scholar
Herre EA, Machado CA, Bermingham E, Nason JD, Windsor DM, McCafferty SS, et al. Molecular phylogenies of figs and their pollinator wasps. J Biogeogr. 1996;23(4):521–30. https://doi.org/10.1111/j.1365-2699.1996.tb00014.x.
Article
Google Scholar
Renoult J, Kjellberg F, Grout C, Santoni S, Khadari B. Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shift in plant-pollinator associations. BMC Evol Biol. 2009;9:248–56. https://doi.org/10.1186/1471-2148-9-248.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rønsted N, Salvo G, Savolainen V. Biogeographical and phylogenetic origins of African fig species (Ficus section Galoglychia). Mol Phylogenet Evol. 2007;43:190–201. https://doi.org/10.1016/j.ympev.2006.12.010.
Article
PubMed
Google Scholar
Rønsted N, Yektaei E, Turk K, Clarkson J, Chase M. 9 Species-Level Phylogenetics of Large Genera: Prospects of Studying Coevolution and Polyploidy. Reconstructing the tree of life: Taxonomy and systematics of species rich taxa. 2006; 129–148. https://doi.org/10.1201/9781420009538.ch9.
Bolger A, Lohse M, Usadel B. Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics (Oxford, England). 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Article
CAS
Google Scholar
Giannoulatou E, Park S-H, Humphreys DT, Ho JWK. Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie. BMC Bioinformatics. 2014;15(16):15–23. https://doi.org/10.1186/1471-2105-15-s16-s15.
Article
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012;19:455–77. https://doi.org/10.1089/cmb.2012.0021.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, et al. GeSeq-versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017;45:6–11. https://doi.org/10.1093/nar/gkx391.
Article
CAS
Google Scholar
Lohse M, Drechsel O, Bock R. OrganellarGenomeDRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 2007;52:267–74. https://doi.org/10.1007/s00294-007-0161-y.
Article
CAS
PubMed
Google Scholar
Kurtz S, Choudhuri J, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale. Nucleic Acids Res. 2001;29:4633–42. https://doi.org/10.1093/nar/29.22.4633.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu X, Adedze Y, Chofong G, Mamadou G, Deng Z, Teng L, et al. Identification of high-efficiency SSR markers for assessing watermelon genetic purity. J Genet. 2018;97(5):1295–306. https://doi.org/10.1007/s12041-018-1027-4.
Article
CAS
PubMed
Google Scholar
Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol. 2021;38(7):3022–7. https://doi.org/10.1093/molbev/msab120.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mayor C, Brudno M, Schwartz J, Poliakov A, Rubin E, Frazer K, et al. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics (Oxford, England). 2000;16:1046–7. https://doi.org/10.1093/bioinformatics/16.11.1046.
Article
CAS
Google Scholar
Katoh K, Standley D, Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. https://doi.org/10.1093/molbev/mst010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Librado PJR, Rozas J. DnaSP v5: A Software for Comprehensive Analysis of DNA Polymorphism Data. Bioinformatics (Oxford, England). 2009;25:1451–2. https://doi.org/10.1093/bioinformatics/btp187.
Article
CAS
Google Scholar