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      The Complete Mitogenome of Elymus sibiricus and Insights Into Its Evolutionary Pattern Based on Simple Repeat Sequences of Seed Plant Mitogenomes

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          Abstract

          The most intriguing characteristics of plant mitochondrial genomes (mitogenomes) include their high variation in both sequence and structure, the extensive horizontal gene transfer (HGT), and the important role they play in hypoxic adaptation. However, the investigation of the mechanisms of hypoxic adaptation and HGT in plant mitochondria remains challenging due to the limited number of sequenced mitogenomes and non-coding nature of the transferred DNA. In this study, the mitogenome of Elymus sibiricus (Gramineae, Triticeae), a perennial grass species native to the Qinghai-Tibet plateau (QTP), was de novo assembled and compared with the mitogenomes of eight Gramineae species. The unique haplotype composition and higher TE content compared to three other Triticeae species may be attributed to the long-term high-altitude plateau adaptability of E. sibiricus. We aimed to discover the connection between mitogenome simple sequence repeats (SSRs) (mt-SSRs) and HGT. Therefore, we predicted and annotated the mt-SSRs of E. sibiricus along with the sequencing of 87 seed plants. The clustering result based on all of the predicted compound mitogenome SSRs (mt-c-SSRs) revealed an expected synteny within systematic taxa and also inter-taxa. The mt-c-SSRs were annotated to 11 genes, among which “(ATA)3agtcaagtcaag (AAT)3” occurred in the nad5 gene of 8 species. The above-mentioned results further confirmed the HGT of mitogenomes sequences even among distant species from the aspect of mt-c-SSRs. Two genes, nad4 and nad7, possessed a vast number of SSRs in their intron regions across the seed plant mitogenomes. Furthermore, five pairs of SSRs developed from the mitogenome of E. sibiricus could be considered as potential markers to distinguish between the species E. sibiricus and its related sympatric species E. nutans.

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          Most cited references57

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            Minimap2: pairwise alignment for nucleotide sequences

            Heng Li (2018)
            Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
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              Inference of Population Structure Using Multilocus Genotype Data

              We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                26 January 2022
                2021
                : 12
                : 802321
                Affiliations
                [1] 1College of Grassland Science and Technology, Sichuan Agricultural University , Chengdu, China
                [2] 2Sichuan Academy of Grassland Science , Chengdu, China
                Author notes

                Edited by: Jorge Duitama, University of Los Andes, Colombia

                Reviewed by: Jing Luo, Yunnan University, China; Daniel Urrea, Universidad del Tolima, Colombia

                *Correspondence: Shiqie Bai, baishiqie@ 123456126.com

                These authors have contributed equally to this work

                This article was submitted to Plant Systematics and Evolution, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2021.802321
                8826237
                35154192
                7672aad8-5d8b-4e63-b0b9-889571c18f66
                Copyright © 2022 Xiong, Yu, Xiong, Zhao, Lei, Liu, Liu, Peng, Zhang, Li, Bai and Ma.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 26 October 2021
                : 27 December 2021
                Page count
                Figures: 9, Tables: 2, Equations: 0, References: 57, Pages: 15, Words: 8493
                Funding
                Funded by: National Natural Science Foundation of China, doi 10.13039/501100001809;
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                elymus sibiricus,seed plant,hgt,ssr,mitochondrial genome
                Plant science & Botany
                elymus sibiricus, seed plant, hgt, ssr, mitochondrial genome

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