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Genomic and evolutionary analysis of the cytochrome P450 gene family in a ground -herb of Amazonian riparian forests

Drielli Canal

University of Campinas

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GCC2024

Brno, Czech Republic

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Original ombrophilous forest cover

Amazonian Forest

Ischnosiphon puberulus

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Ischnosiphon puberulus

Original ombrophilous forest cover

Amazonian Forest

Amazon river

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Ischnosiphon puberulus

Original ombrophilous forest cover

Amazonian Forest

Amazon river

Tapajós river

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Ischnosiphon puberulus

Original ombrophilous forest cover

Amazonian Forest

Amazon river

Tapajós river

Cupari river

Cupari river

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Genomics as key to nowadays challenges

polymodal, short, unpredictable flood pulses

adaptations to rapidly changing conditions

FLOODING PULSE

Flooding gradient (ecological gradient)

Diversity gradient (biological gradient)

monomodal, predictable, long-lasting flood pulses

adaptations to sustained periods of flooding

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One minute: discuss with your neighbor

  • Which specific genes are involved in adaptation to flooded environments increasingly affected by climate change?

Climate Change Forces Local Leaders to Brace for Flooding | Colorado Health Institute

  • How can we identify and investigate the diversity and evolutionary history of genes associated with secondary metabolism and adaptation?
  • How can we expand our understanding of the Marantaceae family and other cultivated species?

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Population sampling in Igapó and Terra firme areas

Water column max. height

Flooding duration

Canopy openness

Terra Firme

0.18 - 1.80 meters

0-3 months

0.73-5.87%

Igapó

6.85 - 8.15 (m)

6-8 months

1.14-14.03%

Flooding conditions

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Chromosome-scale genome assembly

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PacBio HiFi

Omni-C

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2n

Estimated 1C genome size (Mbp)

Assembled 1C genome size (Mbp)

N50 (Mbp)

Mean coverage depth

Mean read length

Mean coverage depth

13

~391

~399

24.7

49 X

~16 Kb

133X

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Gene expression patterns between Terra Firme and Igapó

Sample correlation matrix heatmap for 4,326 differentially expressed transcripts.

FDR rate cut -off of 0.001.

4-fold expression changes.

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Deployment of genomic-wide analysis using Galaxy

https://training.galaxyproject.org/training-material/topics/evolution

https://training.galaxyproject.org/training-material/topics/genome-annotation/

Workflow

  • Data intensive biology for everyone.
  • Open, web-based platform data intensive biology research.
  • Perform, reproduce, and share complete analysis.

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Cytochrome P450s (CYPs)

  • Group of heme b-binding enzymes characterized by the absorption of light at 450 nm by the heme cofactor.
  • Family of enzymes involved in NADPH- and O2-dependent hydroxylation processes.
  • This superfamily is present across various life forms.

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viruses

bacteria

insects

plants

animals

fungi

https://doi.org/10.1111/j.1365-313X.2011.04529.x

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P450s’ role

https://www.mdpi.com/2039-4713/13/3/26; https://doi.org/10.1146/annurev-arplant-042809-112305; https://doi.org/10.1111/j.1365-313X.2011.04529.x

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81, 82

75

​

83

71

810

76

706

705,

703

89

77

73

78

98

705

712,

biosynthesis of natural products

Mafft G-INS-1 algorithm

10.000 bootstrap replicates

Best-fit model: LG+F+R8

A-type

Evolution of plant CYP clans

The diversification of CYPs in the multiple-family clans parallels land plant evolution. The earliest families are key to adaptation to life on land.

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702

97

96

709

86

735

715

714

94

04

51

710

724

720

88

722

74

72

716

707

Evolution of plant CYP clans

Mafft G-INS-1 algorithm

10.000 bootstrap replicates

Best-fit model: LG+F+R8

Non-A-type

fatty acid or sterol metabolism

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A-type Non-a-type

Number of CYP gene family members in the I. puberulus genome

247 214

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47 subfamilies

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Global and differential expression analysis

45 DGEs

Igapó Terra Firme

18

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27

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  • Divergence of Zingiberales from the remaining commelinid monocots

(~ 124 mya).

  • Crown lineages within each family beginning to diversify during the early to mid-Tertiary (~29-64 mya).
  • Important economic species Musa acuminata, Zingiber officinale, Canna indica.

What are the next steps…

https://doi.org/10.1038/s41598-019-50757-1;https://www.mdpi.com/2075-1729/13/5/1087

10.5642/aliso.20062201.49

  • Screening for downregulated genes in flooding-stressed leaves (Igapó).
  • Inhibition of cytochrome P450 may enhance tolerance to flooding stress.

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Acknowledgments

Center for Research on Biodiversity Dynamics and Climate Change

Authors: Clarisse Palma-Silva, Bárbara Simões Santos Leal, Amanda F. Mortati, Cleber Juliano Neves Chaves, Rafael V. Ribeiro, Fabio Pinheiro, Milene Ferro, Diego M. Riaño-Pachón, Jacqueline Salvi de Mattos, Marília Manupella Tavares, Paulo Aecyo, Tami da Costa Cacossi, Jochen Schöngart, Maria Teresa Fernandez Piedade, Thiago André.

Computational analyses were conducted on the Galaxy Server.

Training: https://training.galaxyproject.org/training-material/topics/evolution

https://training.galaxyproject.org/training-material/topics/genome-annotation/

Project: https://www.cbioclima.org/en/

Workflows: https://github.com/diriano and https://github.com/drielliC/Post-Doc-programs