References
- Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27(2):573–580.
- Berg S, Krupinska K, Krause K. 2003. Plastids of three Cuscuta species differing in plastid coding capacity have a common parasite-specific RNA composition. Planta. 218(1):135–142.
- Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120.
- Burland TG. 2000. DNASTAR’s Lasergene sequence analysis software. In: Bioinformatics methods and protocols. Clifton: Springer; p. 71–91.
- Cooke D, Black I. 1987. Biology and control of Cuscuta campestris and other Cuscuta spp.: a bibliographic review. Technical Paper, Department of Agriculture, South Australia.
- Dawson JH, Musselman LJ, Wolswinkel P, Dörr I. 1994. Biology and control of Cuscuta. Rev Weed Sci. 6:265–317.
- Dierckxsens N, Mardulyn P, Smits G. 2016. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18.
- Funk HT, Berg S, Krupinska K, Maier UG, Krause K. 2007. Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol. 7(1):45.
- Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8(3):195–202.
- Katoh K, Kuma K-i, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33(2):511–518.
- Keeling PJ. 2004. Diversity and evolutionary history of plastids and their hosts. Am J Bot. 91(10):1481–1493.
- Krumsiek J, Arnold R, Rattei T. 2007. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics. 23(8):1026–1028.
- Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29(22):4633–4642.
- Li YC, Korol AB, Fahima T, Beiles A, Nevo E. 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol. 11(12):2453–2465.
- Madden T. 2013. The BLAST sequence analysis tool. In: The NCBI handbook [Internet]. 2nd ed. Bethesda: National Center for Biotechnology Information (US).
- Misra S, Harris N. 2005. Using Apollo to browse and edit genome annotations. Curr Protoc Bioinformatics. 12(1):9.5. 1–9.5. 28.
- Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ. 2015. evolution: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274.
- Picardi E, D’Erchia AM, Montalvo A, Pesole G. 2015. Using REDItools to detect RNA editing events in NGS Datasets. Curr Protoc Bioinformatics. 49:12.12.1–12.12.15.
- Sebastian B, Thomas T, Thomas M, Uwe S, Martin M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics. 33(16):2583.
- Sun G, Xu Y, Liu H, Sun T, Zhang J, Hettenhausen C, Shen G, Qi J, Qin Y, Li J, et al. 2018. Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis. Nat Commun. 9(1):2683.