# Orphan genes: Their identification and evolution in plant-parasitic nematodes

Ercan Seçkin, Dominique Colinet, Marc Bailly-Bechet, Edoardo Sarti, Etienne Danchin

► To cite this version:

Ercan Seçkin, Dominique Colinet, Marc Bailly-Bechet, Edoardo Sarti, Etienne Danchin. Orphan genes: Their identification and evolution in plant-parasitic nematodes. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France. hal-04615706v2

HAL Id: hal-04615706

https://hal.science/hal-04615706v2

Submitted on 19 Jun 2024

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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# Orphan genes: Their identification and evolution in plant-parasitic nematodes

Ercan Seçkin, Dominique Colinet, Marc Bailly-Bechet, Edoardo Sarti, Etienne Danchin

► To cite this version:

Ercan Seçkin, Dominique Colinet, Marc Bailly-Bechet, Edoardo Sarti, Etienne Danchin. Orphan genes: Their identification and evolution in plant-parasitic nematodes. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France. hal-04615706v2

HAL Id: hal-04615706

https://hal.science/hal-04615706v2

Submitted on 19 Jun 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# ORPHAN GENES: THEIR IDENTIFICATION AND EVOLUTION IN PLANT PARASITIC NEMATODES

Ercan SEÇKIN*¹,², Dominique COLINET¹, Marc BAILLY-BECHET¹, Edoardo SARTI², Etienne GJ DANCHIN¹

1 ISA - INRAE PACA, Université Côte d'Azur, CNRS, 400 Route des Chappes, 06903, Sophia Antipolis, France.

2 Centre Inria d'Université Côte d'Azur, 2004 Route des Lucioles, 06902, Sophia Antipolis, France.

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

## INTRODUCTION

* **Orphan genes** are genes that have no identifiable homologs. They are systematically found in eukaryotic genomes, and represent up to 30% of the genes [1].

* The **emergence** of such genes is an important mechanism of functional acquisition during evolution. They may originate from duplication or horizontal transfer events followed by **rapid divergence**. Another possibility is that they may emerge from non-genic regions, which is known as **de novo gene birth** [2]. Hence, there is a debate on the real origin of orphan genes [3].

* The most common method for **identifying** orphan genes involves the search for homologues (identification of their absence). Then, their origin can be studied by syntenic approaches. However, these approaches cannot always distinguish between de novo genes and the ones that diverged significantly from their ancestor.

## OBJECTIVES

* We developed a bioinformatics pipeline to **identify orphan genes** and investigate their **emergence dynamics** and possible **de novo origin**.

* The biological purpose is to apply the built pipeline to the genus *Meloidogyne* of root-knot nematodes, which cause a huge global crop loss. The species of this genus secretes parasitism effector, proteins, many of which are encoded by genes having no identifiable homologues [4].

## METHOD & RESULTS

<figure><img src="image_5.png" /><figcaption>**Figure 1: Developed bioinformatics pipeline to identify orphan genes and to study their evolution in Meloidogyne.**</figcaption></figure>

<figure><img src="image_6.png" /><figcaption>**Figure 2: Number of orphan and non orphan genes for 8 Meloidogyne species studied**

Barplot representing the number of orphan genes identified for each of the 8 Meloidogyne species. Each bar corresponds to the total number of genes of each species. Light blue represents orphans and dark blue represents non orphan genes.</figcaption></figure>

<figure><img src="image_7.png" /><figcaption>**Figure 3: Species tree of Meloidogyne species with their closest outgroup species Ppenetrans.**

Species tree with 8 Meloidogyne species corresponding to three different clades (represented at the right of the species) of Meloidogyne genus along with P. penetrans, which is the closest outgroup to this genus. Each ancestral node is represented by a dot. Number of orphan orthogroups emerged in each node is given by a value next to it.</figcaption></figure>

## CONCLUSION & DISCUSSION

* This study introduces a pipeline that combines homology, transcriptomics, and ancestral sequence reconstruction to identify and investigate the origin of orphan genes. This makes it possible to correctly distinguish between orphan genes that have diverged from pre-existing genes and those that have emerged de novo. To date, results indicate that **24%** of *Meloidogyne* genomes consist of **orphan genes**. At least **7%** of these are the result of **de novo gene birth**. Yet, it should be kept in mind that the results depend highly on the quality of genomes in disposition.

* Despite the fact that some effectors in *Meloidogyne* are coded by non-homologous genes, there is still no connection between the orphan genes and their functions in *Meloidogyne*. Thus, we are exploring structural approaches to better characterize these gene-structure-functions associations.

## References

1. Tautz D, Domazet-Lošo T. The evolutionary origin of orphan genes. Nat Rev Genet (2011).

2. Weisman CM. The Origins and Functions of De Novo Genes: Against All Odds? J Mol Evol. (2022).

3. Vakirlis, N. et al. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. eLife (2020).

4. Mitchum et al., Nematode effector proteins: an emerging paradigm of parasitism, New Phytologist (2013).

5. Simão, F.A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics (2015).

6. Nevers Y et al. Multifaceted quality assessment of gene annotation with OMArk. Bioinformatics (2022).

7. https://parasite.wormbase.org/index.html

8. Emms, D.M. et al. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. (2019).

9. Cosentino S, Iwasaki W. SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models, Bioinformatics (2023).

10. Buchfink et al., Fast and sensitive protein alignment using DIAMOND. Nat. Methods (2015).

11. Katoh, K., and Standley, D.M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. (2017).

12. Minh BQ et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Teeling E, editor. Mol Biol Evol. (2020).

13. Comte N et al. Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. Bioinformatics (2020).

14. Jowkar G. et al. ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process. Syst Biol. (2023).

15. Slater, G., and Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005).
# ORPHAN GENES: THEIR IDENTIFICATION AND EVOLUTION IN PLANT PARASITIC NEMATODES

Ercan SEÇKIN*¹,², Dominique COLINET¹, Marc BAILLY-BECHET¹, Edoardo SARTI², Etienne GJ DANCHIN¹

1 ISA - INRAE PACA, Université Côte d'Azur, CNRS, 400 Route des Chappes, 06903, Sophia Antipolis, France.

2 Centre Inria d'Université Côte d'Azur, 2004 Route des Lucioles, 06902, Sophia Antipolis, France.

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

## INTRODUCTION

* **Orphan genes** are genes that have no identifiable homologs. They are systematically found in eukaryotic genomes, and represent up to 30% of the genes [1].

* The **emergence** of such genes is an important mechanism of functional acquisition during evolution. They may originate from duplication or horizontal transfer events followed by **rapid divergence**. Another possibility is that they may emerge from non-genic regions, which is known as **de novo gene birth** [2]. Hence, there is a debate on the real origin of orphan genes [3].

* The most common method for **identifying** orphan genes involves the search for homologues (identification of their absence). Then, their origin can be studied by syntenic approaches. However, these approaches cannot always distinguish between de novo genes and the ones that diverged significantly from their ancestor.

## OBJECTIVES

* We developed a bioinformatics pipeline to **identify orphan genes** and investigate their **emergence dynamics** and possible **de novo origin**.

* The biological purpose is to apply the built pipeline to the genus *Meloidogyne* of root-knot nematodes, which cause a huge global crop loss. The species of this genus secretes parasitism effector, proteins, many of which are encoded by genes having no identifiable homologues [4].

## METHOD & RESULTS

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

## CONCLUSION & DISCUSSION

* This study introduces a pipeline that combines homology, transcriptomics, and ancestral sequence reconstruction to identify and investigate the origin of orphan genes. This makes it possible to correctly distinguish between orphan genes that have diverged from pre-existing genes and those that have emerged de novo. To date, results indicate that **24%** of *Meloidogyne* genomes consist of **orphan genes**. At least **7%** of these are the result of **de novo gene birth**. Yet, it should be kept in mind that the results depend highly on the quality of genomes in disposition.

* Despite the fact that some effectors in *Meloidogyne* are coded by non-homologous genes, there is still no connection between the orphan genes and their functions in *Meloidogyne*. Thus, we are exploring structural approaches to better characterize these gene-structure-functions associations.

## References

1. Tautz D, Domazet-Lošo T. The evolutionary origin of orphan genes. Nat Rev Genet (2011).

2. Weisman CM. The Origins and Functions of De Novo Genes: Against All Odds? J Mol Evol. (2022).

3. Vakirlis, N. et al. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. eLife (2020).

4. Mitchum et al., Nematode effector proteins: an emerging paradigm of parasitism, New Phytologist (2013).

5. Simão, F.A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics (2015).

6. Nevers Y et al. Multifaceted quality assessment of gene annotation with OMArk. Bioinformatics (2022).

7. https://parasite.wormbase.org/index.html

8. Emms, D.M. et al. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. (2019).

9. Cosentino S, Iwasaki W. SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models, Bioinformatics (2023).

10. Buchfink et al., Fast and sensitive protein alignment using DIAMOND. Nat. Methods (2015).

11. Katoh, K., and Standley, D.M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. (2017).

12. Minh BQ et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Teeling E, editor. Mol Biol Evol. (2020).

13. Comte N et al. Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. Bioinformatics (2020).

14. Jowkar G. et al. ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process. Syst Biol. (2023).

15. Slater, G., and Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005).