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Lai C, Wang J, Kan S, Zhang S, Li P, Reeve WG, Wu Z, Zhang Y. Comparative analysis of mitochondrial genomes of Broussonetia spp. (Moraceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing. FRONTIERS IN PLANT SCIENCE 2022; 13:1052151. [PMID: 36531410 PMCID: PMC9751378 DOI: 10.3389/fpls.2022.1052151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
The genus Broussonetia (Moraceae) is comprised of three non-hybrid recognized species that all produce high quality fiber essential in the development of papermaking and barkcloth-making technology. In addition, these species also have medicinal value in several countries. Despite their important economical, medicinal, and ecological values, the complete mitogenome of Broussonetia has not been reported and investigated, which would greatly facilitate molecular phylogenetics, species identification and understanding evolutionary processes. Here, we assembled the first-reported three complete Broussonetia (B. papyrifera, B. kaempferi, and B. monoica) mitochondrial genomes (mitogenome) based on a hybrid strategy using Illumina and Oxford Nanopore Technology sequencing data, and performed comprehensive comparisons in terms of their structure, gene content, synteny, intercellular gene transfer, phylogeny, and RNA editing. Our results showed their huge heterogeneities among the three species. Interestingly, the mitogenomes of B. monoica and B. papyrifera consisted of a single circular structure, whereas the B. kaempferi mitogenome was unique and consisted of a double circular structure. Gene content was consistent except for a few transfer RNA (tRNA) genes. The Broussonetia spp. mitogenomes had high sequence conservation but B. monoica with B. kaempferi contained more synteny blocks and were more related, a finding that was well-supported in organellar phylogeny. Fragments that had been transferred between mitogenomes were detected at plastome hotspots that had integrated under potential mediation of tRNA genes. In addition, RNA editing sites showed great differences in abundance, type, location and efficiency among species and tissues. The availability of these complete gap-free mitogenomes of Broussonetia spp. will provide a valuable genetic resource for evolutionary research and understanding the communications between the two organelle genomes.
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Affiliation(s)
- Chanjuan Lai
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, Guangdong, China
- College of Science, Health, Engineering and Education, Murdoch University, Western Australia, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, Guangdong, China
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, Guangdong, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wayne Gerald Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Western Australia, Australia
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, Guangdong, China
| | - Yonghua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
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Yang J, Chu Q, Meng G, Kong W. The complete chloroplast genome sequences of three Broussonetia species and comparative analysis within the Moraceae. PeerJ 2022; 10:e14293. [PMID: 36340196 PMCID: PMC9632464 DOI: 10.7717/peerj.14293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/03/2022] [Indexed: 01/22/2023] Open
Abstract
Background Species of Broussonetia (family Moraceae) are commonly used to make textiles and high-grade paper. The distribution of Broussonetia papyrifera L. is considered to be related to the spread and location of humans. The complete chloroplast (cp) genomes of B. papyrifera, Broussonetia kazinoki Sieb., and Broussonetia kaempferi Sieb. were analyzed to better understand the status and evolutionary biology of the genus Broussonetia. Methods The cp genomes were assembled and characterized using SOAPdenovo2 and DOGMA. Phylogenetic and molecular dating analysis were performed using the concatenated nucleotide sequences of 35 species in the Moraceae family and were based on 66 protein-coding genes (PCGs). An analysis of the sequence divergence (pi) of each PCG among the 35 cp genomes was conducted using DnaSP v6. Codon usage indices were calculated using the CodonW program. Results All three cp genomes had the typical land plant quadripartite structure, ranging in size from 160,239 bp to 160,841 bp. The ribosomal protein L22 gene (RPL22) was either incomplete or missing in all three Broussonetia species. Phylogenetic analysis revealed two clades. Clade 1 included Morus and Artocarpus, whereas clade 2 included the other seven genera. Malaisia scandens Lour. was clustered within the genus Broussonetia. The differentiation of Broussonetia was estimated to have taken place 26 million years ago. The PCGs' pi values ranged from 0.0005 to 0.0419, indicating small differences within the Moraceae family. The distribution of most of the genes in the effective number of codons plot (ENc-plot) fell on or near the trend line; the slopes of the trend line of neutrality plots were within the range of 0.0363-0.171. These results will facilitate the identification, taxonomy, and utilization of the Broussonetia species and further the evolutionary studies of the Moraceae family.
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Affiliation(s)
- Jinhong Yang
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
| | - Qu Chu
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
| | - Weiqing Kong
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
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Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae. Sci Rep 2022; 12:15800. [PMID: 36138079 PMCID: PMC9500069 DOI: 10.1038/s41598-022-19812-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Petrocodon and Primulina are two characteristic genera of Gesneriaceae that exhibit remarkable species and floral diversity, and high endemism across the Sino-Vietnamese Limestone Karsts. To better understand the evolution of limestone gesneriad plastomes, we report nine complete plastomes of seven Primulina and two Petrocodon which have never been assembled before. The newly generated plastomes range from 152,323 to 153,786 bp in size and display a typical quadripartite structure. To further explore the plastome evolution across Gesneriaceae, we assembled five additional plastomes from public reads data and incorporated 38 complete Gesneriaceae plastomes available online into comparative and phylogenomic analyses. The comparison of 52 Gesneriaceae plastomes reveals that not only Primulina and Petrocodon but all gesneriad genera analyzed are highly conserved in genome size, genome structure, gene contents, IR boundary configurations, and codon usage bias. Additionally, sliding window analyses were implemented across alignments of Primulina and Petrocodon for identifying highly variable regions, providing informative markers for future studies. Meanwhile, the SSRs and long repeats of Gesneriaceae plastomes were characterized, serving as useful data in studying population and repetitive sequence evolutions. The results of plastome phylogenetics represent a preliminary but highly resolved maternal backbone genealogy of Primulina and the Old World subtribes of Gesneriaceae.
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