References
Allen, J. M., Boyd, B., Nguyen, N., Vachaspati, P., Warnow, T., Huang,
D. I., Grady, P. G. S., Bell, K. C., Cronk, Q. C. B., Mugisha, L.,
Pittendrigh, B. R., Soledad Leonardi, M., Reed, D. L., & Johnson, K. P.
(2017). Phylogenomics from Whole Genome Sequences Using aTRAM.Systematic Biology , syw105. https://doi.org/10.1093/sysbio/syw105
Allen, J. M., Huang, D. I., Cronk, Q. C., & Johnson, K. P. (2015).
aTRAM - automated target restricted assembly method: A fast method for
assembling loci across divergent taxa from next-generation sequencing
data. BMC Bioinformatics , 16 (1), 98.
https://doi.org/10.1186/s12859-015-0515-2
Allen, J. M., LaFrance, R., Folk, R. A., Johnson, K. P., & Guralnick,
R. P. (2018). aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS
Data. Evolutionary Bioinformatics , 14 , 117693431877454.
https://doi.org/10.1177/1176934318774546
Bao, E., Jiang, T., & Girke, T. (2014). AlignGraph: Algorithm for
secondary de novo genome assembly guided by closely related references.Bioinformatics , 30 (12), i319–i328.
https://doi.org/10.1093/bioinformatics/btu291
Cameron, D. L., Schröder, J., Penington, J. S., Do, H., Molania, R.,
Dobrovic, A., Speed, T. P., & Papenfuss, A. T. (2017). GRIDSS:
Sensitive and specific genomic rearrangement detection using positional
de Bruijn graph assembly. Genome Research , 27 (12),
2050–2060. https://doi.org/10.1101/gr.222109.117
Capella-Gutierrez, S., Silla-Martinez, J. M., & Gabaldon, T. (2009).
trimAl: A tool for automated alignment trimming in large-scale
phylogenetic analyses. Bioinformatics , 25 (15),
1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Chang, Z., Li, G., Liu, J., Zhang, Y., Ashby, C., Liu, D., Cramer, C.
L., & Huang, X. (2015). Bridger: A new framework for de novo
transcriptome assembly using RNA-seq data. Genome Biology ,16 (1), 30. https://doi.org/10.1186/s13059-015-0596-2
Chikhi, R., & Rizk, G. (2013). Space-efficient and exact de
Bruijn graph representation based on a Bloom filter . 9.
https://doi.org/10.1186/1748-7188-8-22
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J.,
Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., &
de Hoon, M. J. L. (2009). Biopython: Freely available Python tools for
computational molecular biology and bioinformatics.Bioinformatics , 25 (11), 1422–1423.
https://doi.org/10.1093/bioinformatics/btp163
Fér, T., & Schmickl, R. E. (2018). HybPhyloMaker: Target Enrichment
Data Analysis From Raw Reads to Species Trees. Evolutionary
Bioinformatics , 14 , 1176934317742613.
https://doi.org/10.1177/1176934317742613
Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo,
J., … & Rokhsar, D. S. (2012). Phytozome: a comparative platform for
green plant genomics. Nucleic acids research , 40(D1),
D1178-D1186.
Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw,
A. J., Zerega, N. J. C., & Wickett, N. J. (2016). HybPiper: Extracting
coding sequence and introns for phylogenetics from high-throughput
sequencing reads using target enrichment. Applications in Plant
Sciences , 4 (7), 1600016. https://doi.org/10.3732/apps.1600016
Johnson, M. G., Pokorny, L., Dodsworth, S., Botigué, L. R., Cowan, R.
S., Devault, A., Eiserhardt, W. L., Epitawalage, N., Forest, F., Kim, J.
T., Leebens-Mack, J. H., Leitch, I. J., Maurin, O., Soltis, D. E.,
Soltis, P. S., Wong, G. K., Baker, W. J., & Wickett, N. J. (2019). A
Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from
Any Flowering Plant Designed Using k-Medoids Clustering.Systematic Biology , 68 (4), 594–606.
https://doi.org/10.1093/sysbio/syy086
Li, D., Huang, Y., Leung, C.-M., Luo, R., Ting, H.-F., & Lam, T.-W.
(2017). MegaGTA: A sensitive and accurate metagenomic gene-targeted
assembler using iterative de Bruijn graphs. BMC Bioinformatics ,18 (S12), 408. https://doi.org/10.1186/s12859-017-1825-3
Li, M., Wunder, J., Bissoli, G., Scarponi, E., Gazzani, S., Barbaro, E.,
Saedler, H., & Varotto, C. (2008). Development of COS genes as
universally amplifiable markers for phylogenetic reconstructions of
closely related plant species. Cladistics , 24 (5),
727–745. https://doi.org/10.1111/j.1096-0031.2008.00207.x
Li, Z., De La Torre, A. R., Sterck, L., Cánovas, F. M., Avila, C.,
Merino, I., Cabezas, J. A., Cervera, M. T., Ingvarsson, P. K., & Van de
Peer, Y. (2017). Single-Copy Genes as Molecular Markers for Phylogenomic
Studies in Seed Plants. Genome Biology and Evolution , 9(5), 1130–1147. https://doi.org/10.1093/gbe/evx070
Liu, B., Ma, Z., Ren, C., Hodel, R. G. J., Sun, M., Liu, X., Liu, G.,
Hong, D., Zimmer, E. A., & Wen, J. (2021). Capturing single‐copy
nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep
genome skimming data for plant phylogenetics: A case study in Vitaceae.Journal of Systematics and Evolution , 59 (5), 1124–1138.
https://doi.org/10.1111/jse.12806
Palmer, J. D., Jorgensen, R. A., & Thompson, W. F. (1985). CHLOROPLAST
DNA VARIATION AND EVOLUTION IN PISUM: PATTERNS OF CHANGE AND
PHYLOGENETIC ANALYSIS. Genetics , 109 (1), 195–213.
https://doi.org/10.1093/genetics/109.1.195
Palmer, J. D., & Thompson, W. F. (1982). Chloroplast DNA rearrangements
are more frequent when a large inverted repeat sequence is lost.Cell , 29 (2), 537–550. https://doi.org/10.1016/0092-8674
(82)90170-2
Palmer, J. D., & Zamir, D. (1982). Chloroplast DNA evolution and
phylogenetic relationships in Lycopersicon . Proceedings of
the National Academy of Sciences , 79 (16), 5006–5010.
https://doi.org/10.1073/pnas.79.16.5006
Pandey, P., Bender, M. A., Johnson, R., & Patro, R. (2017). deBGR: An
efficient and near-exact representation of the weighted de Bruijn graph.Bioinformatics , 33 (14), i133–i141.
https://doi.org/10.1093/bioinformatics/btx261
Pevzner, P. A., Tang, H., & Waterman, M. S. (2001). An Eulerian path
approach to DNA fragment assembly. Proceedings of the National
Academy of Sciences , 98 (17), 9748–9753.
https://doi.org/10.1073/pnas.171285098
Henriksen, R. A., Zhao L., Korneliussen T.S. (2023). NGSNGS:
next-generation simulator for next-generation sequencing data.Bioinformatics , 39(1), btad041.
Schulz, M. H., Zerbino, D. R., Vingron, M., & Birney, E. (2012). Oases:
Robust de novo RNA-seq assembly across the dynamic range of expression
levels. Bioinformatics , 28 (8), 1086–1092.
https://doi.org/10.1093/bioinformatics/bts094
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J.
M., & Birol, İ. (2009). ABySS: A parallel assembler for short read
sequence data. Genome Research , 19 (6), 1117–1123.
https://doi.org/10.1101/gr.089532.108
Small, R. L., Cronn, R. C., & Wendel, J. F. (2004). Use of nuclear
genes for phylogeny reconstruction in plants. Australian
Systematic Botany , 17 (2), 145. https://doi.org/10.1071/SB03015
Sohn, J., & Nam, J.-W. (2016). The present and future of de novowhole-genome assembly. Briefings in Bioinformatics , bbw096.
https://doi.org/10.1093/bib/bbw096
Straub, S. C. K., Parks, M., Weitemier, K., Fishbein, M., Cronn, R. C.,
& Liston, A. (2012). Navigating the tip of the genomic iceberg:
Next-generation sequencing for plant systematics. American Journal
of Botany , 99 (2), 349–364. https://doi.org/10.3732/ajb.1100335
Wang, X., Liang, D., Jin, W., Tang, M., Shalayiwu, Liu, S., & Zhang, P.
(2020). Out of Tibet: Genomic Perspectives on the Evolutionary History
of Extant Pikas. Molecular Biology and Evolution , 37 (6),
1577–1592. https://doi.org/10.1093/molbev/msaa026
Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: A revolutionary
tool for transcriptomics. Nature Reviews Genetics , 10 (1),
57–63. https://doi.org/10.1038/nrg2484
Weitemier, K., Straub, S. C. K., Cronn, R. C., Fishbein, M., Schmickl,
R., McDonnell, A., & Liston, A. (2014). Hyb-Seq: Combining Target
Enrichment and Genome Skimming for Plant Phylogenomics.Applications in Plant Sciences , 2 (9), 1400042.
https://doi.org/10.3732/apps.1400042
Wen, J., Xie, D.-F., Price, M., Ren, T., Deng, Y.-Q., Gui, L.-J., Guo,
X.-L., & He, X.-J. (2021). Backbone phylogeny and evolution of
Apioideae (Apiaceae): New insights from phylogenomic analyses of
plastome data. Molecular Phylogenetics and Evolution , 161 ,
107183. https://doi.org/10.1016/j.ympev.2021.107183
Wen, J., Yu, Y., Xie, D.-F., Peng, C., Liu, Q., Zhou, S.-D., & He,
X.-J. (2020). A transcriptome-based study on the phylogeny and evolution
of the taxonomically controversial subfamily Apioideae (Apiaceae).Annals of Botany , 125 (6), 937–953.
https://doi.org/10.1093/aob/mcaa011
Wu, F., Mueller, L. A., Crouzillat, D., Pétiard, V., & Tanksley, S. D.
(2006). Combining Bioinformatics and Phylogenetics to Identify Large
Sets of Single-Copy Orthologous Genes (COSII) for Comparative,
Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant
Clade. Genetics , 174 (3), 1407–1420.
https://doi.org/10.1534/genetics.106.062455
Zerbino, D. R., & Birney, E. (2008). Velvet: Algorithms for de novo
short read assembly using de Bruijn graphs. Genome Research ,18 (5), 821–829. https://doi.org/10.1101/gr.074492.107
Zhang, F., Ding, Y., Zhu, C.-D., Zhou, X., Orr, M. C., Scheu, S., &
Luan, Y.-X. (2019). Phylogenomics from low-coverage whole-genome
sequencing. Methods in Ecology and Evolution , 10 (4),
507–517. https://doi.org/10.1111/2041-210X.13145
Zhang, Z., Xie, P., Guo, Y., Zhou, W., Liu, E., & Yu, Y. (2022).
Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research.Molecular Biology and Evolution , 39 (12), msac261.
https://doi.org/10.1093/molbev/msac261
Zhou, W., Soghigian, J., & Xiang, Q.-Y. (Jenny). (2022). A New Pipeline
for Removing Paralogs in Target Enrichment Data. Systematic
Biology , 71 (2), 410–425.
https://doi.org/10.1093/sysbio/syab044