Bioinformatics' usefulness in relation to the Bryophytes

Khushbu Anand; Afroz Alam

doi:10.21276/pt.2025.v2.i1.8

Bioinformatics' usefulness in relation to the Bryophytes

Authors

Khushbu Anand Banasthali Vidyapith Author https://orcid.org/0009-0006-1670-707X
Afroz Alam Banasthali Vidyapith Author https://orcid.org/0000-0001-8575-4677

DOI:

https://doi.org/10.21276/pt.2025.v2.i1.8

Keywords:

Bryophytes, bioinformatics, plant evolution, genomic analysis, transcriptomics, comparative genomics, adaptation

Abstract

Bryophytes, such as mosses, liverworts, and hornworts, are vital species for studying plant evolution because they serve as a bridge between aquatic algae and terrestrial vascular plants. Their haploid-dominant life cycle, basic shape, and absence of intricate vascular systems offer special insights into the evolution of plants. By making it possible to analyze massive genomic, transcriptomic, and proteomic datasets, the development of bioinformatics has significantly advanced the study of bryophytes. This study examines the use of bioinformatics techniques and tools, with a particular emphasis on transcriptome analysis, comparative genomics, genome sequencing, and molecular clock research, to comprehend the evolution of bryophytes. Important new information about the evolution of bryophytes, the dynamics of gene families, and adaptations to terrestrial life has been made possible by these methods. We also discuss the challenges in bryophyte research and outline future directions, emphasizing the need for expanding genomic datasets, integrating multi-omics approaches, and leveraging advanced computational tools.

Author Biographies

Khushbu Anand, Banasthali Vidyapith

Research Scholar, Department of Bioscience and Biotechnology
Afroz Alam, Banasthali Vidyapith

Associate Professor, Department of Bioscience and Biotechnology

References

Fernandez-Pozo N, Haas FB, Gould SB, Rensing SA. An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes. J Exp Bot. 2022; 73(13):4291-4305. https://doi.org/10.1093/jxb/erac052

Rosato M, Kovařík A, Garilleti R, Rosselló JA. Conserved Organisation of 45S rDNA Sites and rDNA Gene Copy Number among Major Clades of Early Land Plants. PLoS One. 2016;11(9):e0162544. https://doi.org/10.1371/journal.pone.0162544

Chang Y, Graham SW. Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set. Am J Bot. 2011; 98(5):839-49. https://doi.org/10.3732/ajb.0900384

Bechteler J, Peñaloza-Bojacá G, Bell D, Burleigh JG, McDaniel SF, Davis EC, Sessa EB, Bippus A, Cargill DC, Chantanoarrapint S, Draper I, Endara L, Forrest LL, Garilleti R, Graham SW, Huttunen S, Lazo JJ, Lara F, Larraín J. Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. Am J Bot. 2023; 110(11): e16249. https://doi.org/10.1002/ajb2.16249

Wang Q, Zhang J, Liu Y, Jia Y, Jiao Y, Xu B, Chen Z. Diversity, phylogeny, and adaptation of bryophytes: Insights from genomic and transcriptomic data. J Exp Bot. 2022; 73(13): 4306-4322. https://doi.org/10.1093/jxb/erac127

Wang ZO, Pollock DD. Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. J. Mol. Evol. Springer. 2007;65:485–95, https://doi.org/10.1007/s00239-007-9018-8

Peters K, Treutler H, Döll S, Kindt ASD, Hankemeier T, Neumann S. Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species. Metabolites. 2019; 9(10):222. https://doi.org/10.3390/metabo9100222

Commisso M, Guarino F, Marchi L, Muto A, Piro A, Degola F. Bryo-Activities: A Review on How Bryophytes Are Contributing to the Arsenal of Natural Bioactive Compounds against Fungi. Plants (Basel). 2021; 10(2):203. https://doi.org/10.3390/plants10020203

Fuselier L, Bougary A, Malott M. From trace evidence to bioinformatics: putting bryophytes into molecular biology education. Biochem Mol Biol Educ. 2011; 39(1):38-46. https://doi.org/10.1002/bmb.20458

Fuselier L, Bougary A, Malott M. From trace evidence to bioinformatics: Putting bryophytes into molecular biology education. Biochem Mol Biol Educ. 2010; 39(1), 38-46. https://doi.org/10.1002/bmb.20458

Wellman C, Osterloff P, Mohiuddin U. Fragments of the earliest land plants. Nature. 2003; 425: 282–285. https://doi.org/10.1038/nature01884

Spitale D, Mair P, Nascimbene J. (2020). Patterns of bryophyte life-forms are predictable across land cover types. Ecol Indic. 2020; 109: 105799. https://doi.org/10.1016/j.ecolind.2019.105799

Peters K, König-Ries B. Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae. Sci Data. 2022; 9: 598 (2022). https://doi.org/10.1038/s41597-022-01691-x

Owens SJ, Blackmore S, Knox RB. Microspores. Evolution and Ontogeny. Kew Bull. 1992; 47(2): 336.

Wang Q-H, Zhang J, Liu Y, Jia Y, Jiao Y-N, Xu B, Chen Z-D. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. J Exp Bot. 2022; 73(13): 4306–4322, https://doi.org/10.1093/jxb/erac127

Rensing SA, Goffinet B, Meyberg R, Wu SZ, Bezanilla M. The Moss Physcomitrium (Physcomitrella) patens: A Model Organism for Non-Seed Plants. Plant Cell. 2020; 32(5):1361-1376. https://doi.org/10.1105/tpc.19.00828

Rensing SA, Lang D, Zimmer AD, et al. The Physcomitrella patens genome reveals evolutionary insights into the earliest land plants. Science. 2008; 319(5859): 64-69. https://doi.org/10.1126/science.1150646

Xiao L, Wang H, Wan P, et al. Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens. BMC Plant Biol. 2011; 11: 177 (2011). https://doi.org/10.1186/1471-2229-11-177

Bowman JL, Kohchi T, Yamato KT, et al. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell. 2017; 171(2):287-304. https://doi.org/10.1016/j.cell.2017.09.030

Liu G-Q, Lian L, Wang W. The Molecular Phylogeny of Land Plants: Progress and Future Prospects. Diversity. 2022; 14(10):782. https://doi.org/10.3390/d14100782.

Downloads

Published

2025-04-29

Data Availability Statement

All data generated or analyzed during this study are included in this published article.

Issue

Vol. 2 No. 1 (2025): 2025, Quarter 1

Section

Articles

License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Copyright and License Terms

Authors who publish with this journal agree to the following terms:

Authors retain the copyright to their work and grant the journal the right of first publication. The work is simultaneously licensed under a Creative Commons Attribution License, permitting others to share it with proper acknowledgement of authorship and its original publication in this journal.
Authors may enter into additional, non-exclusive agreements for distributing the published version of their work (e.g., depositing it in an institutional repository or including it in a book), provided they acknowledge that the work was first published in this journal.

Open Access Policy

License

PhytoTalks is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/

License summary:
You are free to:

1. Share—copy and redistribute the material in any medium or format for any purpose, even commercially.
2. Adapt—remix, transform, and build upon the material for any purpose, even commercially.
3. The licensor cannot revoke these freedoms as long as you follow the license terms.
Under the following terms:
1. Attribution—You must acknowledge appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
2. You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits—this is the only restriction.
Notices:

You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation.

No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights, such as publicity, privacy, or moral rights, may limit how you use the material.

By submitting a manuscript to PhytoTalks, authors confirm that:

The work is original and does not infringe any copyright, trademark, patent, or other rights of third parties.
The work is original and has not been published or submitted for publication elsewhere, except as a preprint.
All necessary permissions for any third-party materials used in the manuscript have been obtained.

Citation Policy

When using or citing articles from PhytoTalks, proper attribution must be given to the original authors and the source, including a DOI link where available.