Phylogenomic Analyses and DNA Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution
Article Swipe
Li‑Na Zhou
,
Shi-Zhen Wu
,
Qing Ma
,
Xiao Wen Jia
,
Pan Li
,
Xin-Jie Jin
,
Yong-hua Zhang
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1002/ece3.72399
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1002/ece3.72399
Moraceae, with its seven tribes, 45 genera, and approximately 1200 species, is of significant value in food, medicine, ecological restoration, and as a source of industrial raw materials. However, determination of the taxonomy and phylogeny of Moraceae species remains challenging due to their diverse morphological features. To address this issue, we sequenced seven complete plastomes and analyzed online datasets for 46 other species at the tribal level within Moraceae. Our analysis revealed that all the plastomes within this family had a typical quadripartite structure and ranged from 158,459 to 162,594 bp in length. Comparative plastome analyses revealed 10 highly variable regions ( ndhF ‐ rpl32 , rps4 ‐ trnT , rps15 ‐ ycf1 , trnC ‐ petN , ycf1 ). A total of 5350 dispersed and tandem repeats along with 4751 simple sequence repeats (SSRs) were identified, highlighting their potential for the development of molecular markers in Moraceae. While the evolutionary rates across the various tribes of Moraceae were found to be similar, the genes ndhK , ndhD , rps2 , and rps12 displayed evidence of positive selection. Codon usage bias was shaped by mutation and selection, with significant natural selection observed on genes such as clpP , ndhC , ndhI , etc. Additionally, 13 optimal codons were identified for 10 genes. This study confirms that the seven tribes within the Moraceae family are monophyletic, with divergence estimated to have occurred approximately 79.43 million years ago. This timing coincides with the formation of modern rainforests and a burst in angiosperm diversity toward the end of the Cretaceous period. Overall, the resolution of Moraceae tribal‐level phylogeny provides a foundational framework for revising taxonomic classifications. Furthermore, our genomic resources will be available for genetic engineering and germplasm exploration within this versatile plant family.
Related Topics
Concepts
Biology
Moraceae
Evolutionary biology
Tandem repeat
Phylogenetics
Clade
Molecular evolution
Adaptive evolution
Phylogenomics
Gene
Genetic diversity
Phylogenetic tree
Genetics
DNA barcoding
DNA sequencing
Chloroplast DNA
Danaus
Taxon
Neutral theory of molecular evolution
Coevolution
Sequence (biology)
Eudicots
Microsatellite
Sequence analysis
Taxonomy (biology)
Divergence (linguistics)
Natural selection
Rate of evolution
Genomics
Convergent evolution
Parallel evolution
Human evolutionary genetics
Mutation rate
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/ece3.72399
- OA Status
- gold
- References
- 71
- OpenAlex ID
- https://openalex.org/W7104551878
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W7104551878Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/ece3.72399Digital Object Identifier
- Title
-
Phylogenomic Analyses and
DNA Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive EvolutionWork title - Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-11-01Full publication date if available
- Authors
-
Li‑Na Zhou, Shi-Zhen Wu, Qing Ma, Xiao Wen Jia, Pan Li, Xin-Jie Jin, Yong-hua ZhangList of authors in order
- Landing page
-
https://doi.org/10.1002/ece3.72399Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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https://doi.org/10.1002/ece3.72399Direct OA link when available
- Concepts
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Biology, Moraceae, Evolutionary biology, Tandem repeat, Phylogenetics, Clade, Molecular evolution, Adaptive evolution, Phylogenomics, Gene, Genetic diversity, Phylogenetic tree, Genetics, DNA barcoding, DNA sequencing, Chloroplast DNA, Danaus, Taxon, Neutral theory of molecular evolution, Coevolution, Sequence (biology), Eudicots, Microsatellite, Sequence analysis, Taxonomy (biology), Divergence (linguistics), Natural selection, Rate of evolution, Genomics, Convergent evolution, Parallel evolution, Human evolutionary genetics, Mutation rateTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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71Number of works referenced by this work
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