Two major chromosome evolution events with unrivaled conserved gene content in pomegranate

Zeynal Akparov; Sabina Hajiyeva; Mehraj Abbasov; Sukhjiwan Kaur; Aladdin Hamwieh; Alsamman M Alsamman; Elchin Hajiyev; Sevda Babayeva; Vusala Izzatullayeva; Ziyafat Mustafayeva; Sabina Mehdiyeva; Orkhan Mustafayev; Ilham Shahmuradov; Peter Kosarev; Victor Solovyev; Asaf Salamov; Abdulqader Jighly

doi:10.3389/fpls.2023.1039211

Two major chromosome evolution events with unrivaled conserved gene content in pomegranate

Front Plant Sci. 2023 Mar 13:14:1039211. doi: 10.3389/fpls.2023.1039211. eCollection 2023.

Authors

Zeynal Akparov¹, Sabina Hajiyeva¹, Mehraj Abbasov^{1

2}, Sukhjiwan Kaur³, Aladdin Hamwieh⁴, Alsamman M Alsamman⁵, Elchin Hajiyev¹, Sevda Babayeva¹, Vusala Izzatullayeva¹, Ziyafat Mustafayeva¹, Sabina Mehdiyeva¹, Orkhan Mustafayev¹, Ilham Shahmuradov^{6

7}, Peter Kosarev⁸, Victor Solovyev⁸, Asaf Salamov^{1

9}, Abdulqader Jighly³

Affiliations

¹ Genetic Resources Institute, Ministry of Science and Education, Baku, Azerbaijan.
² Research Institute of Fruit and Tea, Ministry of Agriculture, Guba, Azerbaijan.
³ Agriculture Victoria, Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.
⁴ Department of Biotechnology, International Centre for Agricultural Research in the Dry Areas(ICARDA), Giza, Egypt.
⁵ Department of Genome Mapping, Agriculture Research Center (ARC), Agricultural Genetic Engineering Research Institute (AGERI), Giza, Egypt.
⁶ Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education, Baku, Azerbaijan.
⁷ Institue of Biophysics, Ministry of Science and Education, Baku, Azerbaijan.
⁸ Softberry Inc., Mount Kisco, NY, United States.
⁹ U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

Abstract

Pomegranate has a unique evolutionary history given that different cultivars have eight or nine bivalent chromosomes with possible crossability between the two classes. Therefore, it is important to study chromosome evolution in pomegranate to understand the dynamics of its population. Here, we de novo assembled the Azerbaijani cultivar "Azerbaijan guloyshasi" (AG2017; 2n = 16) and re-sequenced six cultivars to track the evolution of pomegranate and to compare it with previously published de novo assembled and re-sequenced cultivars. High synteny was observed between AG2017, Bhagawa (2n = 16), Tunisia (2n = 16), and Dabenzi (2n = 18), but these four cultivars diverged from the cultivar Taishanhong (2n = 18) with several rearrangements indicating the presence of two major chromosome evolution events. Major presence/absence variations were not observed as >99% of the five genomes aligned across the cultivars, while >99% of the pan-genic content was represented by Tunisia and Taishanhong only. We also revisited the divergence between soft- and hard-seeded cultivars with less structured population genomic data, compared to previous studies, to refine the selected genomic regions and detect global migration routes for pomegranate. We reported a unique admixture between soft- and hard-seeded cultivars that can be exploited to improve the diversity, quality, and adaptability of local pomegranate varieties around the world. Our study adds body knowledge to understanding the evolution of the pomegranate genome and its implications for the population structure of global pomegranate diversity, as well as planning breeding programs aiming to develop improved cultivars.

Keywords: chromosome evolution; evolution; genomics; pan-genome; pomegranate.

Grants and funding

This work was supported by the Research Program of the Azerbaijan National Academy of Sciences and the Science Development Foundation under the President of the Republic of Azerbaijan (grant no. EİF-2012-2(6)-39/03/3). AS’s work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.