The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes, Structural Characterization, Comparative Analysis, Phylogenomics and Time Divergence

Waqar Ahmad,In-Jung Lee,Abdul Latif Khan,Lubna Lubna,Kyung-Min Kim,Ahmed Al-Harrasi,Sajjad Asaf,Saleem Asif,Rahmatullah Jan

doi:10.3390/ijms23052783

Abstract

The mechanism and course of Triticum plastome evolution is currently unknown; thus, it remains unclear how Triticum plastomes evolved during recent polyploidization. Here, we report the complete plastomes of two polyploid wheat species, Triticum sphaerococcum (AABBDD) and Triticum turgidum subsp. durum (AABB), and compare them with 19 available and complete Triticum plastomes to create the first map of genomic structural variation. Both T. sphaerococcum and T. turgidum subsp. durum plastomes were found to have a quadripartite structure, with plastome lengths of 134,531 bp and 134,015 bp, respectively. Furthermore, diploid (AA), tetraploid (AB, AG) and hexaploid (ABD, AGAm) Triticum species plastomes displayed a conserved gene content and commonly harbored an identical set of annotated unique genes. Overall, there was a positive correlation between the number of repeats and plastome size. In all plastomes, the number of tandem repeats was higher than the number of palindromic and forward repeats. We constructed a Triticum phylogeny based on the complete plastomes and 42 shared genes from 71 plastomes. We estimated the divergence of Hordeum vulgare from wheat around 11.04–11.9 million years ago (mya) using a well-resolved plastome tree. Similarly, Sitopsis species diverged 2.8–2.9 mya before Triticum urartu (AA) and Triticum monococcum (AA). Aegilops speltoides was shown to be the maternal donor of polyploid wheat genomes and diverged ~0.2–0.9 mya. The phylogeny and divergence time estimates presented here can act as a reference framework for future studies of Triticum evolution.

Highlights

Triticeae Dumort. is an economically valuable grass tribe with around 360 species and subspecies in 20–30 genera
Fresh young leaves of T. sphaerococcum (AABBDD) and T. turgidum subsp. durum (AABB) were collected from plants growing in Swat region of Khyber Pakhtunkhwa
The sizes of the T. sphaerococcum and T. turgidum subsp. durum plastomes are 134,015 bp and 134,531 bp, respectively (Figure 1). Both T. sphaerococcum and T. turgidum subsp. durum plastomes were analyzed and compared with 19 associated Triticum cp genomes, with sizes ranging from 133,873 bp (T. aestivum; KJ592713) to 136,886 bp (T. monococcum subsp. monococcum (LC005977)) (Table 1)

Summary

Introduction

Triticeae Dumort. is an economically valuable grass tribe with around 360 species and subspecies in 20–30 genera. Over 10,000 years, one diploid and both tetraploid species have been domesticated, whereas two hexaploid species emerged under cultivation in Eurasia [1]. Hybridization of a cultivated type of tetraploid Triticum turgidum (AABB genomes) with diploid goat grass Aegilops tauschii (DD genome) resulted in hexaploid common wheat, i.e., bread wheat (Triticum aestivum, AABBDD genomes). Triticum zhukovskyi (AAGGAmAm genomes), the second hexaploid wheat, was produced by crossing tetraploid Timopheevi wheat (Triticum timopheevii, AAGG genomes) with diploid einkorn The Emmer lineage of wheat includes T. turgidum and T. aestivum, whereas the Timopheevi lineage includes T. timopheevii and T. zhukovskyi [2]. Triticum urartu (genome AA) contributed the A genome to the Emmer and Timopheevi lineages as the male parent [3,4], whereas Aegilops speltoides (SS genome) contributed the cytoplasm [5] and G genome [6,7] to T. timopheevii as the female parent. Previous research has proposed that the B genome came from one of the other diploid Sitopsis species in the genus Aegilops, i.e., Aegilops searsii (Ss Ss genome), Aegilops sharonensis (Ssh Ssh genome), Aegilops longissima (Sl Sl genome), or Aegilops bicornis (Sb Sb genome) [9]

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Conclusion