Open Access

The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny

Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada

E-mail Address: qxu062@uottawa.ca

Search for more papers by this author

Xiaomeng Zhang

Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada

E-mail Address: xzhan408@uottawa.ca

Search for more papers by this author

Yue Zhang

Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada

E-mail Address: yzhan481@uottawa.ca

Search for more papers by this author

Chunfang Zheng

Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada

E-mail Address: chunfang313@gmail.com

Search for more papers by this author

James H. Leebens-Mack

Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA

E-mail Address: jleebensmack@uga.edu

Search for more papers by this author

Lingling Jin

Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C9, Canada

E-mail Address: lingling.jin@cs.usask.ca

Search for more papers by this author

, and

David Sankoff

Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada

E-mail Address: sankoff@uottawa.ca

Corresponding author.

Search for more papers by this author

https://doi.org/10.1142/S0219720021400084Cited by:1 (Source: Crossref)

This article is part of the issue:

Special Issue: Selected Papers from the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG)
Guest Editors: Rohan B. H. Williams and Louxin Zhang

Abstract

Using RACCROCHE, a method for reconstructing gene content and order of ancestral chromosomes from a phylogeny of extant genomes represented by the gene orders on their chromosomes, we study the evolution of three orders of woody plants. The method retrieves the monoploid complement of each Ancestor in a phylogeny, consisting a complete set of distinct chromosomes, despite some of the extant genomes being recently or historically polyploidized. The three orders are the Sapindales, the Fagales and the Malvales. All of these are independently estimated to have ancestral monoploid number $X = 8$ $X = 8$ .

Keywords:

References

1. Leebens-Mack JH et al., One thousand plant transcriptomes and the phylogenomics of green plants, Nature 574 :679–685, 2019. https://doi.org/10.1038/s41586-019-1693-2 Crossref, Medline, Google Scholar
2. Leebens-Mack JH, Open green genomes: A framework for comparative plant genomics, https://doi.org/10.25585/1488189. Google Scholar
3. Cheng S et al., 10KP: A phylodiverse genome sequencing plan, Gigascience 7(3) :1–9, 2018. https://doi.org/10.1093/gigascience/giy013 Crossref, Medline, Google Scholar
4. Vallée GC, Santos Muñoz D, Sankoff D, Economic importance, taxonomic representation and scientific priority as drivers of genome sequencing projects, BMC Genomics 17(10) :782, 2016. https://doi.org/10.1186/s12864-016-3100-9 Crossref, Medline, Google Scholar
5. Chase MW, Christenhusz MJM, Fay MF, Byng JW, Judd WS, Soltis DE, Mabberley DE, Sennikov AN, Soltis PS, Stevens PF, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV, Botanic J Linnean Soc 181 :1–20, 2016. Crossref, Google Scholar
6. Xu Q, Jin L, Zheng C, Leebens-Mack JH, Sankoff D, RACCROCHE: Ancestral flowering plant chromosomes and gene orders based on generalized adjacencies and chromosomal gene co-occurrences, Lect Not Comput Sci 12686 :97–115, 2021. Crossref, Google Scholar
7. Xu Q, Jin L, Leebens-Mack JH, Sankoff D, Validation of automated chromosome recovery in the reconstruction of ancestral gene order, Algorithms 14(6) :160, 2021. Crossref, Google Scholar
8. Gagnon Y, Blanchette M, El-Mabrouk N, A flexible ancestral genome reconstruction method based on gapped adjacencies, BMC Bioinf 13(19) :S4, 2012. Crossref, Medline, Google Scholar
9. Lyons E and Freeling M, How to usefully compare homologous plant genes and chromosomes as DNA sequences, Plant J 53 :661–673, 2008. Crossref, Medline, Google Scholar
10. Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M, Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids, Plant Physiol 148 :1772–1781, 2008. Crossref, Medline, Google Scholar
11. Lin Y et al., Supporting data for Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics, GigaSci Database, http://dx.doi.org/10.5524/100276. Google Scholar
12. Hu G et al., Two divergent haplotypes from a highly heterozygous lychee genome point to independent domestication events for early and late-maturing cultivars, Nat Gen, 2021 in press. Google Scholar
13. Yang J, Wariss HM, Tao LD, Zhang RG, Yun QZ, Hollingsworth P, Dao ZL, Luo GF, Guo HJ, Ma YP, Sun WB, Supporting data for “De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan of China,” GigaSci Database, http://dx.doi.org/10.5524/100610. Google Scholar
14. Liang Q et al., Supporting data for “The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)”, GigaSci Database, http://dx.doi.org/10.5524/100589. Google Scholar
15. Li W, Zhu XG, Zhang QJ, Li K, Zhang D, Shi C, Gao LZ (2020) SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango, Mangifera Indica, bioRxiv 2020.02.22.960880, https://doi.org/10.1101/2020.02.22.960880. Google Scholar
16. Grattapaglia D, Silva O, Anacardium Occidentale, v0.9, Phytozome 13, https://phytozome-next.jgi.doe.gov/info/Aoccidentale v0.9. Google Scholar
17. Zeng L et al., Whole genomes and transcriptomes reveal adaptation and domestication of pistachio, Genome Biol 20(1) :79, 2019. https://doi.org/10.1186/s13059-019-1686-3 Crossref, Medline, Google Scholar
18. Xu Q et al., The draft genome of sweet orange (Citrus sinensis), Nat Gen 45 :59–66, 2013. https://doi.org/10.1038/ng.2472 Crossref, Medline, Google Scholar
19. Wu GA et al., Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication, Nat Biotechnol 32 :656–662, 2014. https://doi.org/10.1038/nbt.2906 Crossref, Medline, Google Scholar
20. Muellner-Riehl AN, Weeks A, Clayton JW, Buerki S, Nauheimer L, Chiang Y, Cody S, Pell SK, Molecular phylogenetics and molecular clock dating of Sapindales based on plastid rbcL, atpB and trnL-trnF DNA sequences, Taxon 65 :1019–1036, 2016. https://doi.org/10.12705/655.5 Crossref, Google Scholar
21. Wannan BS, Analysis of generic relationships in Anacardiaceae, Blumea 51 :165–195, 2006. Crossref, Google Scholar
22. Mishra B, Gupta DK, Pfenninger M, Hickler T, Langer E, Nam B, Paule J, Sharma R, Ulaszewski B, Warmbier J, Burczyk J, Thines MA, A reference genome of the European beech (Fagus sylvatica L.), GigaScience 7(6) :giy063, 2018. https://doi.org/10.1093/gigascience/giy063 Crossref, Google Scholar
23. Plomion C et al., Oak genome reveals facets of long lifespan, Nat Plants 4 :440–452, 2018. https://doi.org/10.1038/s41477-018-0172-3 Crossref, Medline, Google Scholar
24. Chen S et al., Genome sequence and evolution of Betula platyphylla, Horticult Res 8 :21037, 2021. https://doi.org/10.1038/s41438-021-00481-7 Crossref, Google Scholar
25. Li Y et al., The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding, Horticult Res 8 :54, 2021. https://doi.org/10.1038/s41438-021-00495-1 Crossref, Medline, Google Scholar
26. Ye G, Zhang H, Chen B, Nie S, Liu H, Gao W, Wang H, Gao Y, Gu L, De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth, Plant J 97 :779–794, 2019. https://doi.org/10.1111/tpj.14159 Crossref, Medline, Google Scholar
27. Jia HM et al., The red bayberry genome and genetic basis of sex determination, Plant Biotechnol J 17 :397–409, 2019. https://doi.org/10.1111/pbi.12985 Crossref, Medline, Google Scholar
28. Marrano A et al., High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome, Gigascience 9(5) :giaa050, 2020. https://doi.org/10.1093/gigascience/giaa050 Crossref, Medline, Google Scholar
29. Huang Y et al., The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition, Gigascience 8(5) :giz036, 2019. https://doi.org/10.1093/gigascience/giz036 Crossref, Medline, Google Scholar
30. Kim YM et al., Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants, DNA Res 24 :71–80, 2017. Medline, Google Scholar
31. Li F et al., Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution, Nat Biotechnol 33 :524–30, 2015. Crossref, Medline, Google Scholar
32. Teh BT et al., The draft genome of tropical fruit durian (Durio zibethinus), Nat Gen 49 :1633–1641, 2017. Crossref, Medline, Google Scholar
33. Argout X et al., The genome of Theobroma cacao, Nat Gen 43 :101–108, 2011. Crossref, Medline, Google Scholar
34. NCBI, Herrania Umbratica, Annotation Release 100, 2017, https://www.ncbi.nlm.nih.gov/genome/annotation euk/Herrania umbratica/100/. Google Scholar
35. Islam MS et al., Comparative genomics of two jute species and insight into fibre biogenesis, Nat Plants 3 :16223, 2017. Crossref, Medline, Google Scholar
36. Zhang Y, Zheng C, Islam S, Kim YM, Sankoff D, Branching out to speciation with a birth-and-death model of fractionation: The Malvaceae, IEEE/ACM Trans Comput Biol Bioinf, 2019, early access. Google Scholar
37. Stevens PF, Angiosperm Phylogeny Website, Version 14, 2017, http://www.mobot.org/MOBOT/research/APweb/. Google Scholar

Vol. 19, No. 06

Metrics

Downloaded 398 times

History

Received 1 September 2021

Accepted 5 September 2021

Published: 19 November 2021

Information

This is an Open Access article published by World Scientific Publishing Company. It is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 (CC BY-NC) License which permits use, distribution and reproduction in any medium, provided that the original work is properly cited and is used for non-commercial purposes.

Keywords

PDF download

System Upgrade on Tue, May 28th, 2024 at 2am (EDT)

The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny

Abstract

Recommended