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Marczuk-Rojas JP, Salmerón A, Alcayde A, Isanbaev V, Carretero-Paulet L. Plastid DNA is a major source of nuclear genome complexity and of RNA genes in the orphan crop moringa. BMC PLANT BIOLOGY 2024; 24:437. [PMID: 38773387 PMCID: PMC11110229 DOI: 10.1186/s12870-024-05158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND Unlike Transposable Elements (TEs) and gene/genome duplication, the role of the so-called nuclear plastid DNA sequences (NUPTs) in shaping the evolution of genome architecture and function remains poorly studied. We investigate here the functional and evolutionary fate of NUPTs in the orphan crop Moringa oleifera (moringa), featured by the highest fraction of plastid DNA found so far in any plant genome, focusing on (i) any potential biases in their distribution in relation to specific nuclear genomic features, (ii) their contribution to the emergence of new genes and gene regions, and (iii) their impact on the expression of target nuclear genes. RESULTS In agreement with their potential mutagenic effect, NUPTs are underrepresented among structural genes, although their overall transcription levels and broadness were only lower when involved exonic regions; the occurrence of plastid DNA generally did not result in a broader expression, except among those affected in introns by older NUPTs. In contrast, we found a strong enrichment of NUPTs among specific superfamilies of retrotransposons and several classes of RNA genes, including those participating in the protein biosynthetic machinery (i.e., rRNA and tRNA genes) and a specific class of regulatory RNAs. A significant fraction of NUPT RNA genes was found to be functionally expressed, thus potentially contributing to the nuclear pool. CONCLUSIONS Our results complete our view of the molecular factors driving the evolution of nuclear genome architecture and function, and support plastid DNA in moringa as a major source of (i) genome complexity and (ii) the nuclear pool of RNA genes.
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Affiliation(s)
- Juan Pablo Marczuk-Rojas
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Antonio Salmerón
- Department of Mathematics and Center for the Development and Transfer of Mathematical Research to Industry (CDTIME), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Alfredo Alcayde
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Viktor Isanbaev
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Lorenzo Carretero-Paulet
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain.
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain.
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2
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Zhang Z, Zhao J, Li J, Yao J, Wang B, Ma Y, Li N, Wang H, Wang T, Liu B, Gong L. Evolutionary trajectory of organelle-derived nuclear DNAs in the Triticum/Aegilops complex species. PLANT PHYSIOLOGY 2024; 194:918-935. [PMID: 37847157 PMCID: PMC10828211 DOI: 10.1093/plphys/kiad552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023]
Abstract
Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinyang Yao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yiqiao Ma
- Jilin Academy of Vegetable and Flower Science, Changchun 130033, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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Choi IS, Wojciechowski MF, Steele KP, Hunter SG, Ruhlman TA, Jansen RK. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:389-406. [PMID: 35061308 DOI: 10.1111/tpj.15676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Kelly P Steele
- Division of Science and Mathematics, Arizona State University, Mesa, AZ, 85212, USA
| | - Sarah G Hunter
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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4
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Brandeis M. Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes. Bioessays 2021; 43:e2000256. [PMID: 33860546 DOI: 10.1002/bies.202000256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/10/2022]
Abstract
I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check. Also see the video abstract here: https://youtu.be/aVMvWMpomac.
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Affiliation(s)
- Michael Brandeis
- The Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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Fang J, Wood AM, Chen Y, Yue J, Ming R. Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset. BMC Genomics 2020; 21:398. [PMID: 32532215 PMCID: PMC7291442 DOI: 10.1186/s12864-020-06804-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 06/05/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. RESULTS In this study, a total of more than 74 million Illumina reads for progenitor 'Sunset' were mapped onto transgenic papaya 'SunUp' reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between 'Sunset' and 'SunUp'. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4 × 10- 4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. A total of 3430 nuclear plastid DNA (NUPT) and 2764 nuclear mitochondrial DNA (NUMT) junction sites have been found in 'SunUp', which is proportionally higher than the predicted total NUPT and NUMT junction sites in 'Sunset' (3346 and 2745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by 'SunUp' and 'Sunset'. The average identity between 'SunUp' specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by 'SunUp' and 'Sunset'. Six 'SunUp' organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18 ~ 100%). None of the paired-end spans of mapped 'Sunset' reads were elongated by any 'SunUp' transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions. CONCLUSIONS Comparative whole-genome analyses between 'SunUp' and 'Sunset' provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.
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Affiliation(s)
- Jingping Fang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China.,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew Michael Wood
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Zhang GJ, Dong R, Lan LN, Li SF, Gao WJ, Niu HX. Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants. Int J Mol Sci 2020; 21:ijms21030707. [PMID: 31973163 PMCID: PMC7037861 DOI: 10.3390/ijms21030707] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 11/16/2022] Open
Abstract
The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.
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Affiliation(s)
- Guo-Jun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
| | - Hong-Xing Niu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
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7
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Li SF, Li JR, Wang J, Dong R, Jia KL, Zhu HW, Li N, Yuan JH, Deng CL, Gao WJ. Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution. BMC PLANT BIOLOGY 2019; 19:361. [PMID: 31419941 PMCID: PMC6698032 DOI: 10.1186/s12870-019-1975-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species. RESULTS A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions. CONCLUSIONS These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jia-Rong Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ke-Li Jia
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
- SanQuan Medical College, Xinxiang Medical University, Xinxiang, 453003 China
| | - Hong-Wei Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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8
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Li JR, Li SF, Wang J, Dong R, Zhu HW, Li N, Deng CL, Gao WJ. Characterization of the complete chloroplast genome of Asparagus setaceus. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2639-2640. [PMID: 33365661 PMCID: PMC7706555 DOI: 10.1080/23802359.2019.1643798] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Asparagus setaceus is an important ornamental plant and is important to study the sex chromosome evolution in genus Asparagus. Here the complete chloroplast (cp) genome sequence of A. setaceus was determined. The cpDNA is 156,978 bp in length, contains a large single copy region of 85,311 bp and a small single copy region of 18,641 bp, which was separated by a pair of inverted repeat regions of 26,513 bp each. The cp genome contains 132 genes, including 88 protein-coding genes, 6 ribosomal RNA genes, and 38 transfer RNA genes. Phylogenetic analysis indicates that A. setaceus is closely related to Asparagus officinalis and Asparagus schoberioides.
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Affiliation(s)
- Jia-Rong Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Jin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Hong-Wei Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, China
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9
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Impact of Repetitive Elements on the Y Chromosome Formation in Plants. Genes (Basel) 2017; 8:genes8110302. [PMID: 29104214 PMCID: PMC5704215 DOI: 10.3390/genes8110302] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 12/21/2022] Open
Abstract
In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia. Recent papers showed that both the expansion and shrinkage of the Y chromosome is influenced by sex-specific regulation of repetitive DNA spread. We present a view that the dynamics of Y chromosome formation is an interplay of genetic and epigenetic processes.
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10
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VanBuren R, Wai CM, Zhang J, Han J, Arro J, Lin Z, Liao Z, Yu Q, Wang ML, Zee F, Moore RC, Charlesworth D, Ming R. Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep. Genome Biol 2016; 17:230. [PMID: 27890017 PMCID: PMC5125041 DOI: 10.1186/s13059-016-1095-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 10/31/2016] [Indexed: 11/10/2022] Open
Abstract
Background The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region. Results Diversity is very low for all genes in the X-linked region in the wild dioecious population, with nucleotide diversity πsyn = 0.00017, tenfold lower than the autosomal region (πsyn = 0.0017) and 12-fold lower than the Y-linked region (πsyn = 0.0021). Analysis of the X-linked sequences shows an undivided population, suggesting a geographically wide diversity-reducing event, whereas two subpopulations were observed in the autosomes separating gynodioecy and dioecy and three subpopulations in the Y-linked region separating three male populations. The extremely low diversity in the papaya X-linked region was probably caused by a recent, strong selective sweep before domestication, involving either the spread of a recessive mutation in an X-linked gene that is beneficial to males or a partially dominant mutation that benefitted females or both sexes. Nucleotide diversity in the domesticated X samples is about half that in the wild Xs, probably due to the bottleneck when hermaphrodites were selected during domestication. Conclusions The extreme low nucleotide diversity in the papaya X-linked region is much greater than observed in humans, great apes, and the neo-X chromosome of Drosophila miranda, which show the expected pattern of Y-linked genes < X-linked genes < autosomal genes; papaya shows an unprecedented pattern of X-linked genes < autosomal genes < Y-linked genes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1095-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert VanBuren
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ching Man Wai
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jennifer Han
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jie Arro
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zhicong Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhenyang Liao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX, 75252, USA
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Francis Zee
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Richard C Moore
- Department of Botany, Miami University, Oxford, OH, 45056, USA
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Abstract
Structurally and functionally diverged sex chromosomes have evolved in many animals as well as in some plants. Sex chromosomes represent a specific genomic region(s) with locally suppressed recombination. As a consequence, repetitive sequences involving transposable elements, tandem repeats (satellites and microsatellites), and organellar DNA accumulate on the Y (W) chromosomes. In this paper, we review the main types of repetitive elements, their gathering on the Y chromosome, and discuss new findings showing that not only accumulation of various repeats in non-recombining regions but also opposite processes form Y chromosome. The aim of this review is also to discuss the mechanisms of repetitive DNA spread involving (retro) transposition, DNA polymerase slippage or unequal crossing-over, as well as modes of repeat removal by ectopic recombination. The intensity of these processes differs in non-recombining region(s) of sex chromosomes when compared to the recombining parts of genome. We also speculate about the relationship between heterochromatinization and the formation of heteromorphic sex chromosomes.
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Li SF, Zhang GJ, Yuan JH, Deng CL, Gao WJ. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes. PLANTA 2016; 243:1083-95. [PMID: 26919983 DOI: 10.1007/s00425-016-2485-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 05/03/2023]
Abstract
The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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Vyskot B, Hobza R. The genomics of plant sex chromosomes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:126-35. [PMID: 26025526 DOI: 10.1016/j.plantsci.2015.03.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/27/2015] [Accepted: 03/26/2015] [Indexed: 05/18/2023]
Abstract
Around six percent of flowering species are dioecious, with separate female and male individuals. Sex determination is mostly based on genetics, but morphologically distinct sex chromosomes have only evolved in a few species. Of these, heteromorphic sex chromosomes have been most clearly described in the two model species - Silene latifolia and Rumex acetosa. In both species, the sex chromosomes are the largest chromosomes in the genome. They are hence easily distinguished, can be physically separated and analyzed. This review discusses some recent experimental data on selected model dioecious species, with a focus on S. latifolia. Phylogenetic analyses show that dioecy in plants originated independently and repeatedly even within individual genera. A cogent question is whether there is genetic degeneration of the non-recombining part of the plant Y chromosome, as in mammals, and, if so, whether reduced levels of gene expression in the heterogametic sex are equalized by dosage compensation. Current data provide no clear conclusion. We speculate that although some transcriptome analyses indicate the first signs of degeneration, especially in S. latifolia, the evolutionary processes forming plant sex chromosomes in plants may, to some extent, differ from those in animals.
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Affiliation(s)
- Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic.
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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Genome sequence comparison reveals a candidate gene involved in male–hermaphrodite differentiation in papaya (Carica papaya) trees. Mol Genet Genomics 2014; 290:661-70. [DOI: 10.1007/s00438-014-0955-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
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Vanburen R, Ming R. Dynamic transposable element accumulation in the nascent sex chromosomes of papaya. Mob Genet Elements 2014; 3:e23462. [PMID: 23734293 PMCID: PMC3661139 DOI: 10.4161/mge.23462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/02/2013] [Indexed: 02/03/2023] Open
Abstract
From their inception, Y chromosomes in plants and animals are subjected to the powerful effects of Müller's ratchet, a process spurred by suppression of recombination that results in a rapid accumulation of mutations and repetitive elements. These mutations eventually lead to gene loss and degeneration of the Y chromosome. Y chromosomes in mammals are ancient, whereas most sex chromosomes in plants and many in insects and fish evolved recently. Sex type in papaya is controlled by a pair of nascent sex chromosomes that evolved around 7 million years ago. The papaya X and Yh were recently sequenced, providing valuable insight into the early stages of sex chromosome evolution. Here we discuss the fruits of this work with a focus on the repeat accumulation, gene trafficking and promiscuous DNA sequences found in the slowly degenerating Yh chromosome of papaya.
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Affiliation(s)
- Robert Vanburen
- Department of Plant Biology; University of Illinois at Urbana-Champaign; Urbana, IL USA
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