{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T23:00:01Z","timestamp":1790204401310,"version":"4.1.0"},"reference-count":78,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    <jats:italic>Pyrus calleryana<\/jats:italic>\n                    and\n                    <jats:italic>Pyrus betulifolia<\/jats:italic>\n                    are wild pear germplasm resources characterized by robust stress resistance and diverse application potentials, serving as prominent pear rootstocks in China. However, their mitochondrial genomes (mitogenomes) remain poorly characterized. This study presents the sequencing, assembly, and comprehensive analysis of the complete mitogenomes of\n                    <jats:italic>P. calleryana<\/jats:italic>\n                    and\n                    <jats:italic>P. betulifolia<\/jats:italic>\n                    . The mitogenomes of\n                    <jats:italic>P. betulifolia<\/jats:italic>\n                    (432,496 bp) and\n                    <jats:italic>P. calleryana<\/jats:italic>\n                    (422,567 bp) are circular DNA molecules, with sizes within the known range for\n                    <jats:italic>Pyrus<\/jats:italic>\n                    and smaller than those of cultivated pear. Each genome encodes 35 protein-coding genes (PCGs), 3 rRNA genes, and 19\u201320 tRNA genes, with no core gene loss. The total number of open reading frames (ORFs) is comparable between the two species, each harboring a small set of species-specific ORFs. The mitogenomes of\n                    <jats:italic>P. betulifolia<\/jats:italic>\n                    and\n                    <jats:italic>P. calleryana<\/jats:italic>\n                    contain 139 and 136 simple sequence repeats (SSRs), as well as 520 and 480 dispersed repeats, respectively, with both genomes featuring 20 tandem repeats. Among the PCGs, histidine is the most abundant amino acid and CAU is the most frequently utilized codon (Relative synonymous codon usage = 1.55), while most PCGs in both species are under purifying selection (Ka\/Ks&amp;lt; 1). Whole-genome alignment revealed a single nucleotide polymorphism (SNP) in both the core energy metabolism genes\n                    <jats:italic>nad2<\/jats:italic>\n                    and\n                    <jats:italic>atp1.<\/jats:italic>\n                    Additionally, 54 mitochondrial plastid DNA fragments and 616 predicted C-to-U RNA-editing sites were identified in both mitogenomes. Collinearity analysis revealed extensive genome rearrangements in the two species. Phylogenetic trees constructed using both\n                    <jats:italic>Pyrus<\/jats:italic>\n                    -specific and\n                    <jats:italic>Rosaceae<\/jats:italic>\n                    -wide datasets demonstrate that\n                    <jats:italic>P. betulifolia<\/jats:italic>\n                    and\n                    <jats:italic>P. calleryana<\/jats:italic>\n                    cluster with other\n                    <jats:italic>Pyrus<\/jats:italic>\n                    species, showing the closest relationship to\n                    <jats:italic>P. ussuriensis<\/jats:italic>\n                    \u00d7\n                    <jats:italic>P. communis<\/jats:italic>\n                    \u2018Zhongai1\u2019, albeit with limited resolution. This study provides high-quality mitogenome assemblies for\n                    <jats:italic>P. calleryana<\/jats:italic>\n                    and\n                    <jats:italic>P. betulifolia<\/jats:italic>\n                    , revealing coexisting structural variations and highly conserved sequences, and thereby offers a significant genetic resource for the\n                    <jats:italic>Rosaceae<\/jats:italic>\n                    family that will facilitate further investigations into the molecular diversity and genetic evolution of wild pears.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1906069","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:20:56Z","timestamp":1790086856000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Assembly and comparative analysis of the complete mitochondrial genomes of Pyrus calleryana Decne. and Pyrus betulifolia Bunge"],"prefix":"10.3389","volume":"17","author":[{"given":"Huan","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Advanced Agriculture and Life Sciences, Weifang University, Weifang","place":["Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongliang","family":"Ji","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Life Sciences, Weifang University, Weifang","place":["Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutong","family":"Chi","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Life Sciences, Weifang University, Weifang","place":["Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinge","family":"Li","sequence":"additional","affiliation":[{"name":"Qingdao Key Lab of Genetic Improvement and Breeding of Horticultural Plants, Pear Engineering Technology Research Institute, College of Horticulture, Qingdao Agricultural University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ran","family":"Wang","sequence":"additional","affiliation":[{"name":"Qingdao Key Lab of Genetic Improvement and Breeding of Horticultural Plants, Pear Engineering Technology Research Institute, College of Horticulture, Qingdao Agricultural University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingjie","family":"Yang","sequence":"additional","affiliation":[{"name":"Qingdao Key Lab of Genetic Improvement and Breeding of Horticultural Plants, Pear Engineering Technology Research Institute, College of Horticulture, Qingdao Agricultural University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dingli","family":"Li","sequence":"additional","affiliation":[{"name":"Qingdao Key Lab of Genetic Improvement and Breeding of Horticultural Plants, Pear Engineering Technology Research Institute, College of Horticulture, Qingdao Agricultural University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1436","DOI":"10.1093\/molbev\/msq029","article-title":"Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)","volume":"27","author":"Alverson","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"2583","DOI":"10.1093\/bioinformatics\/btx198","article-title":"MISA-web: a web server for microsatellite prediction","volume":"33","author":"Beier","year":"2017","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.3390\/genes14020526","article-title":"De novo assembly and comparative analysis of the complete mitochondrial genome of Chaenomeles speciosa (Sweet) Nakai revealed the existence of two structural isomers","volume":"14","author":"Cao","year":"2023","journal-title":"Genes"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1194","DOI":"10.1101\/289660","article-title":"TBtools: an integrative toolkit developed for interactive analyses of big biological data","volume":"13","author":"Chen","year":"2020","journal-title":"Mol. Plant"},{"key":"B7","doi-asserted-by":"publisher","first-page":"7762","DOI":"10.1093\/nar\/gkv784","article-title":"High speed BLASTN: an accelerated MegaBLAST search tool","volume":"43","author":"Chen","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B8","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.1080\/23802359.2020.1800429","article-title":"Characterization of the complete chloroplast genome of Pyrus pyrifolia 'Yunhongli No. 1'","volume":"5","author":"Cheng","year":"2020","journal-title":"Mitochondrial DNA B. Resour."},{"key":"B9","doi-asserted-by":"publisher","first-page":"2424","DOI":"10.1080\/23802359.2019.1598802","article-title":"The complete chloroplast genome of Korean Pyrus ussuriensis Maxim. (Rosaceae): providing genetic background of two types of P. ussuriensis","volume":"4","author":"Cho","year":"2019","journal-title":"Mitochondrial DNA B. Resour."},{"key":"B10","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1093\/gbe\/evt069","article-title":"Plant mitochondrial genome evolution can be explained by DNA repair mechanisms","volume":"5","author":"Christensen","year":"2013","journal-title":"Genome Biol. Evol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1080\/23802359.2017.1413300","article-title":"The complete mitochondrial genome of Wonwhang (Pyrus pyrifolia)","volume":"2","author":"Chung","year":"2017","journal-title":"Mitochondrial DNA B. Resour."},{"key":"B12","doi-asserted-by":"publisher","first-page":"2773","DOI":"10.1093\/molbev\/msy176","article-title":"High and variable rates of repeat-mediated mitochondrial genome rearrangement in a genus of plants","volume":"35","author":"Cole","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"2","DOI":"10.5962\/p.287338","article-title":"The rise and fall of the ornamental Callery pear tree","volume":"74","author":"Culley","year":"2017","journal-title":"Arnoldia"},{"key":"B14","doi-asserted-by":"publisher","first-page":"956","DOI":"10.1641\/B571108","article-title":"The beginning of a new invasive plant: A history of the ornamental Callery pear in the United States","volume":"57","author":"Culley","year":"2007","journal-title":"BioScience"},{"key":"B15","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"De Coster","year":"2018","journal-title":"Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1111\/nph.18334","article-title":"Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions","volume":"236","author":"Fan","year":"2022","journal-title":"New Phytol."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/genes12121970","article-title":"Assembly of the complete mitochondrial genome of Chinese plum (Prunus salicina): characterization of genome recombination and RNA editing sites","volume":"12","author":"Fang","year":"2021","journal-title":"Genes"},{"key":"B18","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1186\/s12870-023-04338-0","article-title":"Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis","volume":"23","author":"Gao","year":"2023","journal-title":"BMC Plant Biol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1006\/jmbi.2001.5102","article-title":"Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles","volume":"313","author":"Gautheret","year":"2001","journal-title":"J. Mol. Biol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"W59","DOI":"10.1093\/nar\/gkz238","article-title":"OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes","volume":"47","author":"Greiner","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B21","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1186\/s12864-025-11892-4","article-title":"De novo assembly and characterization of Aria alnifolia chloroplast and mitochondrial genomes reveal homologous conformational changes mediated by repeat regions and gene transfer","volume":"26","author":"Ha","year":"2025","journal-title":"BMC Genomics"},{"key":"B22","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1007\/s11032-025-01591-z","article-title":"Mitochondrial candidate gene, orf206, for cytoplasmic male sterility in Pear (Pyrus pyrifolia)","volume":"45","author":"Han","year":"2025","journal-title":"Mol. Breed."},{"key":"B23","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1186\/s12906-021-03392-1","article-title":"A review of pears (Pyrus spp.), ancient functional food for modern times","volume":"21","author":"Hong","year":"2021","journal-title":"BMC Complement Med. Ther."},{"key":"B24","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1186\/s12864-021-07967-7","article-title":"A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers","volume":"22","author":"Hong","year":"2021","journal-title":"BMC Genomics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","article-title":"NextPolish: a fast and efficient genome polishing tool for long-read assembly","volume":"36","author":"Hu","year":"2020","journal-title":"Bioinformatics"},{"key":"B26","doi-asserted-by":"publisher","first-page":"219","DOI":"10.17520\/biods.2018319","article-title":"Advancing phylogeography with chloroplast DNA markers","volume":"27","author":"Hu","year":"2019","journal-title":"Biodivers. Sci."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.3390\/genes8010005","article-title":"RNA editing and its molecular mechanism in plant organelles","volume":"8","author":"Ichinose","year":"2017","journal-title":"Genes"},{"key":"B28","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2024.1468596","article-title":"Chloroplast genome sequencing and divergence analysis of 18 Pyrus species: insights into intron length polymorphisms and evolutionary processes","volume":"15","author":"Kim","year":"2024","journal-title":"Front. Genet."},{"key":"B30","doi-asserted-by":"publisher","first-page":"4633","DOI":"10.1093\/nar\/29.22.4633","article-title":"Reputer: the manifold applications of repeat analysis on a genomic scale","volume":"29","author":"Kurtz","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"B31","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"B32","doi-asserted-by":"publisher","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","article-title":"Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences","volume":"32","author":"Li","year":"2016","journal-title":"Bioinformatics"},{"key":"B33","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/j.freeradbiomed.2016.03.033","article-title":"The role of mitochondria in plant development and stress tolerance","volume":"100","author":"Liberatore","year":"2016","journal-title":"Free Radic. Biol. Med."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1266797","article-title":"Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis","volume":"14","author":"Liu","year":"2023","journal-title":"Front. Plant Sci."},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2025.1599464","article-title":"Assembly and comparative analysis of the complete mitochondrial genome of Indocalamus longiauritus","volume":"16","author":"Liu","year":"2025","journal-title":"Front. Plant Sci."},{"key":"B36","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1093\/molbev\/msp011","article-title":"Comparative analysis of structural diversity and sequence evolution in plant mitochondrial genes transferred to the nucleus","volume":"26","author":"Liu","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2023.1329060","article-title":"Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond (Prunus tenella)","volume":"14","author":"Liu","year":"2024","journal-title":"Front. Genet."},{"key":"B38","first-page":"145","article-title":"Pear rootstocks","volume-title":"Rootstocks for Fruit Crops","author":"Lombard","year":"1987"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1132551","article-title":"Assembly and analysis of the first complete mitochondrial genome of Punica granatum and the gene transfer from chloroplast genome","volume":"14","author":"Lu","year":"2023","journal-title":"Front. Plant Sci."},{"key":"B40","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1111\/j.1469-8137.2010.03195.x","article-title":"Recombination and the maintenance of plant organelle genome stability","volume":"186","author":"Marechal","year":"2010","journal-title":"New Phytol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"517","DOI":"10.21273\/JASHS.126.5.517","article-title":"ISSR analysis of cultivars of pear and suitability of molecular markers for clone discrimination","volume":"126","author":"Monte-Corvo","year":"2001","journal-title":"J. Am. Soc Hortic. Sci."},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-6-96","article-title":"PREP-Mt: predictive RNA editor for plant mitochondrial genes","volume":"6","author":"Mower","year":"2005","journal-title":"BMC Bioinf."},{"key":"B43","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030619","article-title":"NGS QC toolkit: a toolkit for quality control of next generation sequencing data","volume":"7","author":"Patel","year":"2012","journal-title":"PloS One"},{"key":"B45","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.mito.2020.03.008","article-title":"Mitochondria in parasitic plants","volume":"52","author":"Petersen","year":"2020","journal-title":"Mitochondrion"},{"key":"B46","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1007\/BF02772108","article-title":"Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components","volume":"15","author":"Porebski","year":"1997","journal-title":"Plant Mol. Biol. Rep."},{"key":"B47","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1186\/s12864-020-07061-4","article-title":"Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome","volume":"21","author":"Putintseva","year":"2020","journal-title":"BMC Genomics"},{"key":"B48","doi-asserted-by":"publisher","first-page":"2084","DOI":"10.1093\/nar\/28.10.2084","article-title":"Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces","volume":"28","author":"Romero","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"B49","doi-asserted-by":"publisher","first-page":"7737","DOI":"10.1093\/nar\/14.19.7737","article-title":"Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons","volume":"14","author":"Sharp","year":"1986","journal-title":"Nucleic Acids Res."},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/541097","article-title":"Origin, domestication, and dispersing of pear (Pyrus spp.)","volume":"2014","author":"Silva","year":"2014","journal-title":"Adv. Agric."},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001241","article-title":"Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates","volume":"10","author":"Sloan","year":"2012","journal-title":"PloS Biol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/gbe\/evu253","article-title":"History of plastid DNA insertions reveals weak deletion and at mutation biases in angiosperm mitochondrial genomes","volume":"6","author":"Sloan","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1111\/tpj.14578","article-title":"Plant organellar RNA editing: what 30 years of research has revealed","volume":"101","author":"Small","year":"2020","journal-title":"Plant J."},{"key":"B54","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1007\/s00122-004-1871-x","article-title":"Development and mapping of microsatellite (SSR) markers in wheat","volume":"110","author":"Song","year":"2005","journal-title":"Theor. Appl. Genet."},{"key":"B55","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/s41438-021-00562-7","article-title":"Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants","volume":"8","author":"Song","year":"2021","journal-title":"Hortic. Res."},{"key":"B56","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1186\/s12915-022-01383-3","article-title":"Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity","volume":"20","author":"Sun","year":"2022","journal-title":"BMC Biol."},{"key":"B57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2503\/jjshs.65.1","article-title":"Characteristics of mitochondrial particles in relation to flooding tolerance in pear rootstocks","volume":"65","author":"Tamura","year":"1996","journal-title":"J. Japan. Soc Hortic. Sci."},{"key":"B58","doi-asserted-by":"publisher","first-page":"370","DOI":"10.13925\/j.cnki.gsxb.20160211","article-title":"Advances in the research on phylogeny of the genus Pyrus and the origin of pear cultivars native to East Asia","volume":"34","author":"Teng","year":"2017","journal-title":"Int. J. Fruit Sci."},{"key":"B59","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.tibs.2019.10.004","article-title":"Striking diversity of mitochondria-specific translation processes across eukaryotes","volume":"45","author":"Waltz","year":"2020","journal-title":"Trends Biochem. Sci."},{"key":"B60","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1038\/s41598-022-24327-x","article-title":"Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia","volume":"13","author":"Wang","year":"2023","journal-title":"Sci. Rep."},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.3390\/biom14080912","article-title":"Morphological structure identification, comparative mitochondrial genomics and population genetic analysis toward exploring interspecific variations and phylogenetic implications of Malus baccata 'ZA' and other species","volume":"14","author":"Wang","year":"2024","journal-title":"Biomolecules"},{"key":"B62","doi-asserted-by":"publisher","first-page":"2040","DOI":"10.1093\/molbev\/msm133","article-title":"Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA","volume":"24","author":"Wang","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PloS Comput. Biol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"B65","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s13059-018-1452-y","article-title":"Diversification and independent domestication of Asian and European pears","volume":"19","author":"Wu","year":"2018","journal-title":"Genome Biol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1534\/g3.118.200948","article-title":"Repeats of unusual size in plant mitochondrial genomes: identification, incidence and evolution","volume":"9","author":"Wynn","year":"2019","journal-title":"G3 Genes Genomes Genet."},{"key":"B67","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1093\/oxfordjournals.molbev.a026236","article-title":"Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models","volume":"17","author":"Yang","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1016\/j.cub.2021.11.053","article-title":"The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides","volume":"32","author":"Yu","year":"2022","journal-title":"Curr. Biol."},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2025.1558619","article-title":"Assembly and analysis of the complete mitochondrial genome of Prunus davidiana (Rosaceae)","volume":"16","author":"Zhang","year":"2025","journal-title":"Front. Plant Sci."},{"key":"B70","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/S1672-0229(07)60007-2","article-title":"KaKs_Calculator: calculating Ka and Ks through model selection and model averaging","volume":"4","author":"Zhang","year":"2006","journal-title":"Genomics Proteomics Bioinf."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-244","article-title":"RCircos: an R package for Circos 2D track plots","volume":"14","author":"Zhang","year":"2013","journal-title":"BMC Bioinf."},{"key":"B72","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1186\/s12870-024-05780-4","article-title":"Assembly and comparative analysis of the first complete mitochondrial genome of Astragalus membranaceus (Fisch.) Bunge: an invaluable traditional Chinese medicine","volume":"24","author":"Zhang","year":"2024","journal-title":"BMC Plant Biol."},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24098366","article-title":"Assembly of the complete mitochondrial genome of Pereskia aculeata revealed that two pairs of repetitive elements mediated the recombination of the genome","volume":"24","author":"Zhang","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"B74","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1016\/j.bbrc.2012.02.101","article-title":"ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments","volume":"419","author":"Zhang","year":"2012","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B75","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1186\/s12870-024-05969-7","article-title":"Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer","volume":"25","author":"Zhang","year":"2025","journal-title":"BMC Plant Biol."},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.3390\/genes15080968","article-title":"A global identification of protein disulfide isomerases from 'duli' pear (Pyrus betulaefolia) and their expression profiles under salt stress","volume":"15","author":"Zhang","year":"2024","journal-title":"Genes"},{"key":"B77","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.ympev.2014.07.009","article-title":"Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences","volume":"80","author":"Zheng","year":"2014","journal-title":"Mol. Phylogenet. Evol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1186\/s12870-024-05645-w","article-title":"Deciphering the multi-partite mitochondrial genome of Crataegus pinnatifida: insights into the evolution and genetics of cultivated hawthorn","volume":"24","author":"Zhu","year":"2024","journal-title":"BMC Plant Biol."}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1906069\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T22:07:13Z","timestamp":1790201233000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1906069\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,21]]},"references-count":78,"alternative-id":["10.3389\/fpls.2026.1906069"],"URL":"https:\/\/doi.org\/10.3389\/fpls.2026.1906069","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,21]]},"article-number":"1906069"}}