1. Yabuno, T. 1981, Cytological relationship between Echinochloa
oryzicola Vasing and the french strain of E. phyllopogon stapf
subsp oryzicola (Vasing) Koss, Cytologia, 46, 393–6.
Downloaded from https://academic.oup.com/dnaresearch/article/30/5/dsad023/7334457 by Kyoto Univeristy user on 13 November 2023
Figure 5. Genetic relationship for E. phyllopogon. (A) PCA, (B) phylogenetic tree using the maximum likelihood method, and (C) the genetic structure of
K = 4 and 5. Dot colours in (A) and (B) were consistent with the horizontal bar colours in (C).
Genome assembly of Echinochloa phyllopogon
24. Rastas, P. 2017, Lep-MAP3: robust linkage mapping even for
low-coverage whole genome sequencing data, Bioinformatics, 33,
3726–32.
25. Tang, H., Zhang, X., Miao, C., et al. 2015, ALLMAPS: robust scaffold ordering based on multiple maps, Genome Biol., 16, 3.
26. Manni, M., Berkeley, M.R., Seppey, M., Simão, F.A., and Zdobnov,
E.M. 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, 4647–54.
27. Ondov, B.D., Treangen, T.J., Melsted, P., et al. 2016, Mash: fast
genome and metagenome distance estimation using MinHash, Genome Biol., 17, 132.
28. Bao, W., Kojima, K.K., and Kohany, O. 2015, Repbase update, a
database of repetitive elements in eukaryotic genomes, Mob. DNA,
6, 11.
29. Brůna, T., Hoff, K.J., Lomsadze, A., Stanke, M., and Borodovsky,
M. 2021, BRAKER2: automatic eukaryotic genome annotation
with GeneMark-EP+ and AUGUSTUS supported by a protein database, NAR Genom. Bioinform., 3, lqaa108.
30. Kawahara, Y., de la Bastide, M., Hamilton, J.P., et al. 2013, Improvement of the Oryza sativa Nipponbare reference genome using
next generation sequence and optical map data, Rice (New York,
N.Y.), 6, 4.
31. Jiao, Y., Peluso, P., Shi, J., et al. 2017, Improved maize reference
genome with single-molecule technologies, Nature, 546, 524–7.
32. Huerta-Cepas, J., Szklarczyk, D., Heller, D., et al. 2019, eggNOG
50: a hierarchical, functionally and phylogenetically annotated
orthology resource based on 5090 organisms and 2502 viruses,
Nucleic Acids Res., 47, D309–14.
33. UniProt Consortium. 2021, UniProt: the universal protein
knowledgebase in 2021, Nucleic Acids Res., 49, D480–9.
34. Huerta-Cepas, J., Forslund, K., Coelho, L.P., et al. 2017, Fast
genome-wide functional annotation through orthology assignment
by eggNOG-mapper, Mol. Biol. Evol., 34, 2115–22.
35. Buchfink, B., Reuter, K., and Drost, H.-G. 2021, Sensitive protein
alignments at tree-of-life scale using DIAMOND, Nat. Methods,
18, 366–8.
36. Emms, D.M. and Kelly, S. 2019, OrthoFinder: phylogenetic
orthology inference for comparative genomics, Genome Biol., 20,
238.
37. Shumate, A. and Salzberg, S.L. 2020, Liftoff: accurate mapping of
gene annotations, Bioinformatics, 37, 1639–43.
38. Adrian Alexa, J. R. 2017, topGO. Bioconductor.
39. Alexa, A., Rahnenführer, J., and Lengauer, T. 2006, Improved
scoring of functional groups from gene expression data by
decorrelating GO graph structure, Bioinformatics, 22, 1600–7.
40. Li, H. 2018, Minimap2: pairwise alignment for nucleotide
sequences, Bioinformatics, 34, 3094–100.
41. Cabanettes, F. and Klopp, C. 2018, D-GENIES: dot plot large
genomes in an interactive, efficient and simple way, PeerJ, 6, e4958.
42. Wang, Y., Tang, H., Debarry, J.D., et al. 2012, MCScanX: a toolkit
for detection and evolutionary analysis of gene synteny and collinearity, Nucleic Acids Res., 40, e49.
43. Bandi, V., and Gutwin, C. 2020, Interactive exploration of genomic
conservation. In: Proceedings of the 46th Graphics Interface Conference on Proceedings of Graphics Interface 2020.
44. Cingolani, P., Platts, A., Wang, L.L., et al. 2012, A program
for annotating and predicting the effects of single nucleotide
polymorphisms, SnpEff: SNPs in the genome of Drosophila
melanogaster strain w1118; iso-2; iso-3, Fly, 6, 80–92.
45. Chang, C.C., Chow, C.C., Tellier, L.C.A.M., Vattikuti, S., Purcell,
S.M., and Lee, J.J. 2015, Second-generation PLINK: rising to the
challenge of larger and richer datasets, GigaScience, 4, 1–16.
46. Stamatakis, A. 2014, RAxML version 8: a tool for phylogenetic
analysis and post-analysis of large phylogenies, Bioinformatics, 30,
1312–3.
47. Alexander, D.H., Novembre, J., and Lange, K. 2009, Fast modelbased estimation of ancestry in unrelated individuals, Genome
Res., 19, 1655–64.
Downloaded from https://academic.oup.com/dnaresearch/article/30/5/dsad023/7334457 by Kyoto Univeristy user on 13 November 2023
2. Yamasue, Y. 2001, Strategy of Echinochloa oryzicola Vasing for
survival in flooded rice, Weed Biol. Manag., 1, 28–36.
3. Yasuda, K., Mori, K., and Nakayama, Y. 2020, A tetraploid Echinochloa
with plagiotropic tillers: its distribution and habitat in the northern
part of the main island of Japan, Weed Biol. Manag., 20, 82–8.
4. Iwakami, S., Endo, M., Saika, H., et al. 2014, Cytochrome P450
CYP81A12 and CYP81A21 are associated with resistance to two
acetolactate synthase inhibitors in Echinochloa phyllopogon, Plant
Physiol., 165, 618–29.
5. Iwakami, S., Kamidate, Y., Yamaguchi, T., et al. 2019, CYP81A
P450s are involved in concomitant cross-resistance to acetolactate
synthase and acetyl-CoA carboxylase herbicides in Echinochloa
phyllopogon, New Phytol., 221, 2112–22.
6. Suda, H., Kubo, T., Yoshimoto, Y., et al. 2023, Transcriptionally
linked simultaneous overexpression of P450 genes for broad-spectrum herbicide resistance, Plant Physiol., 192, 3017–29.
7. Ye, C.-Y., Wu, D., Mao, L., et al. 2020, The genomes of the
allohexaploid echinochloa crus-galli and its progenitors provide
insights into polyploidization-driven adaptation, Mol. Plant, 13,
1298–310.
8. Wu, D., Shen, E., Jiang, B., et al. 2022, Genomic insights into the
evolution of Echinochloa species as weed and orphan crop, Nat.
Commun., 13, 689.
9. Nurk, S., Koren, S., Rhie, A., et al. 2022, The complete sequence of
a human genome, Science, 376, 44–53.
10. Huang, Z., Xu, Z., Bai, H., et al. 2023, Evolutionary analysis of
a complete chicken genome, Proc. Natl. Acad. Sci. U.S.A., 120,
e2216641120.
11. Bowyer, P., Currin, A., Delneri, D., and Fraczek, M.G. 2022,
Telomere-to-telomere genome sequence of the model mould pathogen Aspergillus fumigatus, Nat. Commun., 13, 5394.
12. Kurokochi, H., Tajima, N., Sato, M.P., et al. 2023, Telomere-totelomere genome assembly of matsutake (Tricholoma matsutake),
DNA Res., 30, dsad006.
13. Bliznina, A., Masunaga, A., Mansfield, M.J., et al. 2021, Telomereto-telomere assembly of the genome of an individual Oikopleura
dioica from Okinawa using Nanopore-based sequencing, BMC
Genom., 22, 222.
14. Giguere, D.J., Bahcheli, A.T., Slattery, S.S., et al. 2022, Telomere-totelomere genome assembly of Phaeodactylum tricornutum, PeerJ,
10, e13607.
15. Tsuji, R., Fischer, A.J., Yoshino, M., Roel, A., Hill, J.E., and
Yamasue, Y. 2003, Herbicide-resistant late watergrass (Echinochloa
phyllopogon): similarity in morphological and amplified fragment
length polymorphism traits, Weed Sci., 51, 740–7.
16. Marçais, G. and Kingsford, C. 2011, A fast, lock-free approach for
efficient parallel counting of occurrences of k-mers, Bioinformatics,
27, 764–70.
17. Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., and Li, H. 2021,
Haplotype-resolved de novo assembly using phased assembly
graphs with hifiasm, Nat. Methods, 18, 170–5.
18. Marçais, G., Delcher, A.L., Phillippy, A.M., Coston, R., Salzberg,
S.L., and Zimin, A. 2018, MUMmer4: a fast and versatile genome
alignment system, PLoS Comput. Biol., 14, e1005944.
19. Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S., and Hoekstra,
H.E. 2012, Double digest RADseq: an inexpensive method for de
novo SNP discovery and genotyping in model and non-model species, PLoS One, 7, e37135.
20. Shirasawa, K., Hirakawa, H., and Isobe, S. 2016, Analytical workflow of double-digest restriction site-associated DNA sequencing
based on empirical and in silico optimization in tomato, DNA Res.,
23, 145–53.
21. Langmead, B. and Salzberg, S.L. 2012, Fast gapped-read alignment
with Bowtie 2, Nat. Methods, 9, 357–9.
22. Danecek, P., Bonfield, J.K., Liddle, J., et al. 2021, Twelve years of
SAMtools and BCFtools, GigaScience, 10, giab008.
23. Danecek, P., Auton, A., Abecasis, G., et al.; 1000 Genomes Project
Analysis Group. 2011, The variant call format and VCFtools, Bioinformatics, 27, 2156–8.
10
56. Shirasawa, K., Itai, A., and Isobe, S. 2021, Genome sequencing
and analysis of two early-flowering cherry (Cerasus × kanzakura)
varieties, ‘Kawazu-zakura’ and ‘Atami-zakura’, DNA Res., 28,
dsab026.
57. Shirasawa, K., Nishio, S., Terakami, S., Botta, R., Marinoni,
D.T., and Isobe, S. 2021, Chromosome-level genome assembly
of Japanese chestnut (Castanea crenata Sieb et Zucc) reveals
conserved chromosomal segments in woody rosids, DNA Res.,
28, dsab016.
58. Huang, C., Ding, S., Zhang, H., Du, H., and An, L. 2011, CIPK7 is
involved in cold response by interacting with CBL1 in Arabidopsis
thaliana, Plant Sci., 181, 57–64.
59. Cheong, Y.H., Kim, K.-N., Pandey, G.K., Gupta, R., Grant, J.J., and
Luan, S. 2003, CBL1, a calcium sensor that differentially regulates
salt, drought, and cold responses in Arabidopsis, Plant Cell, 15,
1833–45.
60. Yasuda, S., Aoyama, S., Hasegawa, Y., Sato, T., and Yamaguchi,
J. 2017, Arabidopsis CBL-interacting protein kinases regulate
carbon/nitrogen-nutrient response by phosphorylating ubiquitin ligase ATL31, Mol. Plant, 10, 605–18.
61. Kolukisaoglu, U., Weinl, S., Blazevic, D., Batistic, O., and Kudla,
J. 2004, Calcium sensors and their interacting protein kinases: genomics of the arabidopsis and rice CBL-CIPK signaling networks,
Plant Physiol., 134, 43–58.
Downloaded from https://academic.oup.com/dnaresearch/article/30/5/dsad023/7334457 by Kyoto Univeristy user on 13 November 2023
48. Bennetzen, J.L., Schmutz, J., Wang, H., et al. 2012, Reference genome sequence of the model plant Setaria, Nat. Biotechnol., 30,
555–61.
49. Sakai, H., Lee, S.S., Tanaka, T., et al. 2013, Rice Annotation Project
Database (RAP-DB): an integrative and interactive database for
rice genomics, Plant Cell Physiol., 54, e6.
50. Liu, J., Seetharam, A.S., Chougule, K., et al. 2020, Gapless assembly
of maize chromosomes using long-read technologies, Genome
Biol., 21, 121.
51. Wang, B., Yang, X., Jia, Y., et al. 2022, High-quality Arabidopsis
thaliana Genome Assembly with Nanopore and HiFi Long Reads,
Genom. Proteom. Bioinform., 20, 4–13.
52. Deng, Y., Liu, S., Zhang, Y., et al. 2022, A telomere-to-telomere
gap-free reference genome of watermelon and its mutation library
provide important resources for gene discovery and breeding, Mol.
Plant, 15, 1268–84.
53. Rice, E.S. and Green, R.E. 2019, New approaches for genome assembly and scaffolding, Annu. Rev. Anim. Biosci., 7, 17–40.
54. Fierst, J.L. 2015, Using linkage maps to correct and scaffold de
novo genome assemblies: methods, challenges, and computational
tools, Front. Genet., 6, 220.
55. Gutiérrez-Valencia, J., Fracassetti, M., Berdan, E.L., et al. 2022, Genomic analyses of the Linum distyly supergene reveal convergent
evolution at the molecular level, Curr. Biol., 32, 4360–4371.e6.
M.P. Sato et al.
...