Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications
BackgroundThe cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineer...
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| Teanga: | English |
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Frontiers Media S.A.
2024-03-01
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| Sraith: | Frontiers in Plant Science |
| Ábhair: | |
| Rochtain ar líne: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1347945/full |
| _version_ | 1827324810584129536 |
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| author | Jing Liu Jing Liu Yuqing Feng Cheng Chen Jing Yan Xinyu Bai Huiru Li Chen Lin Yinan Xiang Yinan Xiang Wen Tian Zhechen Qi Jing Yu Xiaoling Yan |
| author_facet | Jing Liu Jing Liu Yuqing Feng Cheng Chen Jing Yan Xinyu Bai Huiru Li Chen Lin Yinan Xiang Yinan Xiang Wen Tian Zhechen Qi Jing Yu Xiaoling Yan |
| author_sort | Jing Liu |
| collection | DOAJ |
| description | BackgroundThe cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.ResultsWe sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations.ConclusionOur study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics. |
| first_indexed | 2024-03-07T14:03:28Z |
| format | Article |
| id | doaj.art-d6f072e8910b410ea886cc3b39f9e5e6 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-07T14:03:28Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d6f072e8910b410ea886cc3b39f9e5e62024-03-07T04:32:27ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-03-011510.3389/fpls.2024.13479451347945Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implicationsJing Liu0Jing Liu1Yuqing Feng2Cheng Chen3Jing Yan4Xinyu Bai5Huiru Li6Chen Lin7Yinan Xiang8Yinan Xiang9Wen Tian10Zhechen Qi11Jing Yu12Xiaoling Yan13Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, ChinaCollege of Life Science, Shanghai Normal University, Shanghai, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, ChinaAnimal Plant and Food Inspection Center of Nanjing Customs District, Nanjing, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, ChinaCollege of Life Science, Shanghai Normal University, Shanghai, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, ChinaBackgroundThe cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.ResultsWe sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations.ConclusionOur study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.https://www.frontiersin.org/articles/10.3389/fpls.2024.1347945/fullCactaceaeclonal reproductiongene transferhomologous recombinationmitochondrial genomeOpuntia cochenillifera |
| spellingShingle | Jing Liu Jing Liu Yuqing Feng Cheng Chen Jing Yan Xinyu Bai Huiru Li Chen Lin Yinan Xiang Yinan Xiang Wen Tian Zhechen Qi Jing Yu Xiaoling Yan Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications Frontiers in Plant Science Cactaceae clonal reproduction gene transfer homologous recombination mitochondrial genome Opuntia cochenillifera |
| title | Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications |
| title_full | Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications |
| title_fullStr | Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications |
| title_full_unstemmed | Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications |
| title_short | Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications |
| title_sort | genomic insights into the clonal reproductive opuntia cochenillifera mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications |
| topic | Cactaceae clonal reproduction gene transfer homologous recombination mitochondrial genome Opuntia cochenillifera |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1347945/full |
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