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Lee HJ, Lee Y, Lee SC, Kim CK, Kang JN, Kwon SJ, Kang SH. Comparative analysis of mitochondrial genomes of Schisandra repanda and Kadsura japonica. FRONTIERS IN PLANT SCIENCE 2023; 14:1183406. [PMID: 37469771 PMCID: PMC10352487 DOI: 10.3389/fpls.2023.1183406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023]
Abstract
The family Schisandraceae is a basal angiosperm plant group distributed in East and Southeast Asia and includes many medicinal plant species such as Schisandra chinensis. In this study, mitochondrial genomes (mitogenomes) of two species, Schisandra repanda and Kadsura japonica, in the family were characterized through de novo assembly using sequencing data obtained with Oxford Nanopore and Illumina sequencing technologies. The mitogenomes of S. repanda were assembled into one circular contig (571,107 bp) and four linear contigs (10,898-607,430 bp), with a total of 60 genes: 38 protein-coding genes (PCGs), 19 tRNA genes, and 3 rRNA genes. The mitogenomes of K. japonica were assembled into five circular contigs (211,474-973,503 bp) and three linear contigs (8,010-72,712 bp), with a total of 66 genes: 44 PCGs, 19 tRNA genes, and 3 rRNA genes. The mitogenomes of the two species had complex structural features with high repeat numbers and chloroplast-derived sequences, as observed in other plant mitogenomes. Phylogenetic analysis based on PCGs revealed the taxonomical relationships of S. repanda and K. japonica with other species from Schisandraceae. Finally, molecular markers were developed to distinguish between S. repanda, K. japonica, and S. chinensis on the basis of InDel polymorphisms present in the mitogenomes. The mitogenomes of S. repanda and K. japonica will be valuable resources for molecular and taxonomic studies of plant species that belong to the family Schisandraceae.
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Affiliation(s)
- Hyo Ju Lee
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | | | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Soo-Jin Kwon
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
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Structure and Phylogeny of Chloroplast and Mitochondrial Genomes of a Chlorophycean Algae Pectinodesmus pectinatus (Scenedesmaceae, Sphaeropleales). LIFE (BASEL, SWITZERLAND) 2022; 12:life12111912. [PMID: 36431047 PMCID: PMC9698225 DOI: 10.3390/life12111912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
Pectinodesmus pectinatus is a green alga of commercial interest in sewage purification. Clarification of its organelle genomes is helpful for genetic manipulation, taxonomic revisions and evolutionary research. Here, de novo sequencing was used to determine chloroplast genome and mitochondrial genome of P. pectinatus strain F34. The chloroplast genome was composed of a large single-copy (LSC) region of 99,156 bp, a small single-copy (SSC) region of 70,665 bp, and a pair of inverted repeats (IRs) with a length of 13,494 bp each separated by LSC and SSC. The chloroplast genome contained 69 protein-coding genes, 25 transfer-RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes. The mitochondrial genome was 32,195 bp in length and consisted of 46 unique genes, including 16 protein-coding genes, 27 tRNA genes and 3 rRNA genes. The predominant mutations in organelle genomes were T/A to G/C transitions. Phylogenic analysis indicated P. pectinatus was a sister species to Tetradesmus obliquus and Hariotina sp. within the Pectinodesmus genus. In analysis with CGView Comparison Tool, P. pectinatus organelle genomes displayed the highest sequence similarity with that of T. obliquus. These findings advanced research on the taxonomy and phylogeny of Chlorophyceae algae and particularly revealed the role of P. pectinatus in microalgae evolution.
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Fang J, Xu X, Chen Q, Lin A, Lin S, Lei W, Zhong C, Huang Y, He Y. The complete mitochondrial genome of Isochrysis galbana harbors a unique repeat structure and a specific trans-spliced cox1 gene. Front Microbiol 2022; 13:966219. [PMID: 36238593 PMCID: PMC9551565 DOI: 10.3389/fmicb.2022.966219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The haptophyte Isochrysis galbana is considered as a promising source for food supplements due to its rich fucoxanthin and polyunsaturated fatty acids content. Here, the I. galbana mitochondrial genome (mitogenome) was sequenced using a combination of Illumina and PacBio sequencing platforms. This 39,258 bp circular mitogenome has a total of 46 genes, including 20 protein-coding genes, 24 tRNA genes and two rRNA genes. A large block of repeats (~12.7 kb) was segregated in one region of the mitogenome, accounting for almost one third of the total size. A trans-spliced gene cox1 was first identified in I. galbana mitogenome and was verified by RNA-seq and DNA-seq data. The massive expansion of tandem repeat size and cis- to trans-splicing shift could be explained by the high mitogenome rearrangement rates in haptophytes. Strict SNP calling based on deep transcriptome sequencing data suggested the lack of RNA editing in both organelles in this species, consistent with previous studies in other algal lineages. To gain insight into haptophyte mitogenome evolution, a comparative analysis of mitogenomes within haptophytes and among eight main algal lineages was performed. A core gene set of 15 energy and metabolism genes is present in haptophyte mitogenomes, consisting of 1 cob, 3 cox, 7 nad, 2 atp and 2 ribosomal genes. Gene content and order was poorly conserved in this lineage. Haptophyte mitogenomes have lost many functional genes found in many other eukaryotes including rps/rpl, sdh, tat, secY genes, which make it contain the smallest gene set among all algal taxa. All these implied the rapid-evolving and more recently evolved mitogenomes of haptophytes compared to other algal lineages. The phylogenetic tree constructed by cox1 genes of 204 algal mitogenomes yielded well-resolved internal relationships, providing new evidence for red-lineages that contained plastids of red algal secondary endosymbiotic origin. This newly assembled mitogenome will add to our knowledge of general trends in algal mitogenome evolution within haptophytes and among different algal taxa.
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Affiliation(s)
- Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
- *Correspondence: Jingping Fang,
| | - Xiuming Xu
- College of Life Science, Fujian Normal University, Fuzhou, China
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Xiuming Xu,
| | - Qinchang Chen
- College of Life Science, Fujian Normal University, Fuzhou, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
| | - Aiting Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Wen Lei
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Cairong Zhong
- College of Life Science, Fujian Normal University, Fuzhou, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
| | - Yongji Huang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Yongjin He
- College of Life Science, Fujian Normal University, Fuzhou, China
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Kim D, Lee J, Cho CH, Kim EJ, Bhattacharya D, Yoon HS. Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs. BMC Biol 2022; 20:2. [PMID: 34996446 PMCID: PMC8742464 DOI: 10.1186/s12915-021-01200-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium. Results Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences. Conclusion Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01200-3.
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Affiliation(s)
- Dongseok Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, South Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Eun Jeung Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea.
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The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes. Int J Biol Macromol 2020; 162:209-219. [DOI: 10.1016/j.ijbiomac.2020.06.142] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 01/14/2023]
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Mower JP. Variation in protein gene and intron content among land plant mitogenomes. Mitochondrion 2020; 53:203-213. [PMID: 32535166 DOI: 10.1016/j.mito.2020.06.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/24/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022]
Abstract
The functional content of the mitochondrial genome (mitogenome) is highly diverse across eukaryotes. Among land plants, our understanding of the variation in mitochondrial gene and intron content is improving from concerted efforts to densely sample mitogenomes from diverse land plants. Here I review the current state of knowledge regarding the diversity in content of protein genes and introns in the mitogenomes of all major land plant lineages. Mitochondrial protein gene content is largely conserved among mosses and liverworts, but it varies substantially among and within other land plant lineages due to convergent losses of genes encoding ribosomal proteins and, to a lesser extent, genes for proteins involved in cytochrome c maturation and oxidative phosphorylation. Mitochondrial intron content is fairly stable within each major land plant lineage, but highly variable among lineages, resulting from occasional gains and many convergent losses over time. Trans-splicing has evolved dozens of times in various vascular plant lineages, particularly those with relatively higher rates of mitogenomic rearrangement. Across eukaryotes, mitochondrial protein gene and intron content has been shaped massive convergent evolution.
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Affiliation(s)
- Jeffrey P Mower
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE.
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Orton LM, Fitzek E, Feng X, Grayburn WS, Mower JP, Liu K, Zhang C, Duvall MR, Yin Y. Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3361-3373. [PMID: 32206790 DOI: 10.1093/jxb/eraa149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/19/2020] [Indexed: 05/22/2023]
Abstract
The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on land plant terrestrialization. Here, we report the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157 548 bp) and SAG 698-1a (165 372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215 954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 ORFs. These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase, and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is probably from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element.
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Affiliation(s)
- Lauren M Orton
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Elisabeth Fitzek
- Biology/Computational Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology-CeBiTec, Bielefeld, Germany
| | - Xuehuan Feng
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - W Scott Grayburn
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Yanbin Yin
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
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Turmel M, Otis C, Lemieux C. Complete mitogenome of the streptophyte green alga Coleochaete scutata (Coleochaetophyceae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:4209-4210. [PMID: 33366386 PMCID: PMC7707659 DOI: 10.1080/23802359.2019.1693300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We have sequenced the mitogenome of Coleochaete scutata strain SAG 110.80M. This mitogenome is the largest among the streptophyte green algae examined to date. At 242,024 bp, it is 4.3-fold larger than the mitogenome of Chaetosphaeridium globosum, the only other mitogenome available for the Coleochaetophyceae. This size difference is mainly explained by differences in the abundance of introns and in the length of intergenic regions containing vestiges of coding sequences thought to be of foreign origin. With 31 group I and 26 group II introns, the C. scutata mitogenome is the most intron-rich organelle genome known among streptophyte algae.
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Affiliation(s)
- Monique Turmel
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Christian Otis
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Claude Lemieux
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
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Dynamic evolution of mitochondrial genomes in Trebouxiophyceae, including the first completely assembled mtDNA from a lichen-symbiont microalga (Trebouxia sp. TR9). Sci Rep 2019; 9:8209. [PMID: 31160653 PMCID: PMC6547736 DOI: 10.1038/s41598-019-44700-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Trebouxiophyceae (Chlorophyta) is a species-rich class of green algae with a remarkable morphological and ecological diversity. Currently, there are a few completely sequenced mitochondrial genomes (mtDNA) from diverse Trebouxiophyceae but none from lichen symbionts. Here, we report the mitochondrial genome sequence of Trebouxia sp. TR9 as the first complete mtDNA sequence available for a lichen-symbiont microalga. A comparative study of the mitochondrial genome of Trebouxia sp. TR9 with other chlorophytes showed important organizational changes, even between closely related taxa. The most remarkable change is the enlargement of the genome in certain Trebouxiophyceae, which is principally due to larger intergenic spacers and seems to be related to a high number of large tandem repeats. Another noticeable change is the presence of a relatively large number of group II introns interrupting a variety of tRNA genes in a single group of Trebouxiophyceae, which includes Trebouxiales and Prasiolales. In addition, a fairly well-resolved phylogeny of Trebouxiophyceae, along with other Chlorophyta lineages, was obtained based on a set of seven well-conserved mitochondrial genes.
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Zheng F, Liu H, Jiang M, Xu Z, Wang Z, Wang C, Du F, Shen Z, Wang B. The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration. Gene 2018; 673:225-238. [PMID: 29933020 DOI: 10.1016/j.gene.2018.06.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 04/21/2018] [Accepted: 06/15/2018] [Indexed: 11/19/2022]
Abstract
The complete mitochondrial genome is greatly important for studies on genetic structure and phylogenetic relationship at various taxonomic levels. To obtain information about the evolutionary trends of mtDNA in the Ulvophyceae and also to gain insights into the phylogenetic relationships between ulvophytes and other chlorophytes, we determined the mtDNA sequence of Caulerpa lentillifera (sea grape) using de novo mitochondrial genome sequencing. The complete genomic DNA of C. lentillifera was circular and 209,034 bp in length, and it was the largest green-algal mitochondrial genome sequenced to date, with a low gene density of 65.2%, which is reminiscent of the "expanded" pattern of evolution exhibited by embryophyte mtDNAs. The C. lentillifera mtDNA consisted of a typical set of 17 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 42 putative open reading frames (ORFs) and 29 introns, which had homologs in green-algal mtDNAs displaying an "ancestral" or a "reduced-derived" pattern of evolution. The overall base composition of its mitochondrial genome was 24.19% for A, 24.94% for T, 25.80% for G, 25.07% for C and 50.87% for GC. The mitochondrial genome of C. lentillifera was characterized by numerous small intergenic regions and introns, which was clearly different from other green algae. With the exception of the NADH dehydrogenase subunit 6 (ND6), ND1, ATP and three tRNA genes (tRNA-His, tRNA-Thr and tRNA-Ala), all other mitochondrial genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we inferred the complete mtDNA sequence of C. lentillifera, an ulvophyte belonging to a distinct, early-diverging lineage. Taken together, our data offered useful information for the studies on phylogenetic hypotheses and phylogenetic relationships of C. lentillifera within the Chlorophyta.
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Affiliation(s)
- Fengrong Zheng
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Hongzhan Liu
- Marine College of Shandong University, Weihai 264209, China.
| | - Meijing Jiang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongjun Xu
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongxing Wang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Claire Wang
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Fei Du
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Zhen Shen
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Bo Wang
- First Institute of Oceanography SOA, Qingdao 266061, China.
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Mikhailyuk T, Lukešová A, Glaser K, Holzinger A, Obwegeser S, Nyporko S, Friedl T, Karsten U. New Taxa of Streptophyte Algae (Streptophyta) from Terrestrial Habitats Revealed Using an Integrative Approach. Protist 2018; 169:406-431. [PMID: 29860113 PMCID: PMC6071840 DOI: 10.1016/j.protis.2018.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 10/25/2022]
Abstract
Two new genera (Streptosarcina and Streptofilum) and three new species (Streptosarcina arenaria, S. costaricana and Streptofilum capillatum) of streptophyte algae were detected in cultures isolated from terrestrial habitats of Europe and Central America and described using an integrative approach. Additionally, a strain isolated from soil in North America was identified as Hormidiella parvula and proposed as an epitype of this species. The molecular phylogeny based on 18S rRNA and rbcL genes, secondary structure of ITS-2, as well as the morphology of vegetative and reproductive stages, cell ultrastructure, ecology and distribution of the investigated strains were assessed. The new genus Streptosarcina forms a sister lineage to the genus Hormidiella (Klebsormidiophyceae). Streptosarcina is characterized by packet-like (sarcinoid) and filamentous thalli with true branching and a cell organization typical for Klebsormidiophyceae. Streptofilum forms a separate lineage within Streptophyta. This genus represents an easily disintegrating filamentous alga which exhibits a cell coverage of unique structure: layers of submicroscopic scales of piliform shape covering the plasmalemma and exfoliate inside the mucilage envelope surrounding cells. The implications of the discovery of the new taxa for understanding evolutionary tendencies in the Streptophyta, a group of great evolutionary interest, are discussed.
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Affiliation(s)
- Tatiana Mikhailyuk
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Tereschenkivska Str. 2, Kyiv 01004, Ukraine.
| | - Alena Lukešová
- Biology Centre of the Czech Academy of Sciences, v.v.i., Institute of Soil Biology, Na Sádkách 7, České Budějovice CZ-37005, Czech Republic
| | - Karin Glaser
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
| | - Andreas Holzinger
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - Sabrina Obwegeser
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - Svetlana Nyporko
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Tereschenkivska Str. 2, Kyiv 01004, Ukraine
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae, Georg-August University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Ulf Karsten
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
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Carvalho EL, Wallau GL, Rangel DL, Machado LC, Pereira AB, Victoria FDC, Boldo JT, Pinto PM. Phylogenetic positioning of the Antarctic alga Prasiola crispa (Trebouxiophyceae) using organellar genomes and their structural analysis. JOURNAL OF PHYCOLOGY 2017; 53:908-915. [PMID: 28394430 DOI: 10.1111/jpy.12541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 01/09/2017] [Indexed: 06/07/2023]
Abstract
Antarctica is one of the most difficult habitats for sustaining life on earth; organisms that live there have developed different strategies for survival. Among these organisms is the green alga Prasiola crispa, belonging to the class Trebouxiophyceae. The literature on P. crispa taxonomy is scarce, and many gaps in the evolutionary relationship with its closest relatives remain. The goal of this study was to analyze the evolutionary relationships between P. crispa and other green algae using plastid and mitochondrial genomes. In addition, we analyzed the synteny conservation of these genomes of P. crispa with those of closely related species. Based on the plastid genome, P. crispa grouped with Prasiolopsis sp. SAG 84.81, another Trebouxiophyceaen species from the Prasiola clade. Based on the mitochondrial genome analysis, P. crispa grouped with other Trebouxiophyceaen species but had a basal position. The structure of the P. crispa chloroplast genome had low synteny with Prasiolopsis sp. SAG 84.81, despite some conserved gene blocks. The same was observed in the mitochondrial genome compared with Coccomyxa subellipsoidea C-169. We were able to establish the phylogenetic position of P. crispa with other species of Trebouxiophyceae using its genomes. In addition, we described the plasticity of these genomes using a structural analysis. The plastid and mitochondrial genomes of P. crispa will be useful for further genetic studies, phylogenetic analysis and resource protection of P. crispa as well as for further phylogenetic analysis of Trebouxiophyceaen green algae.
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Affiliation(s)
- Evelise Leis Carvalho
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia Centro de Pesquisas Aggeu Magalhães, Fiocruz, Recife, 50740-465, Brazil
| | - Darlene Lopes Rangel
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | - Laís Ceschini Machado
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | | | | | | | - Paulo Marcos Pinto
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
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Satjarak A, Burns JA, Kim E, Graham LE. Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis. JOURNAL OF PHYCOLOGY 2017; 53:601-615. [PMID: 28191642 DOI: 10.1111/jpy.12521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha-proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early-diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida). We constructed de novo mitochondrial genomes for two prasinophyte algal species, Pyramimonas parkeae and Cymbomonas tetramitiformis, representing the prasinophyte clade. Comparisons of genome structure and gene order between these species and to those of other prasinophytes revealed that the mitochondrial genomes of P. parkeae and C. tetramitiformis are more similar to each other than to other prasinophytes, consistent with other molecular inferences of the close relationship between these two species. Phylogenetic analyses using the inferred amino acid sequences of mitochondrial and chloroplast protein-coding genes resolved a clade consisting of P. parkeae and C. tetramitiformis; and this group (representing the prasinophyte clade I) branched with the clade II, consistent with previous studies based on the use of nuclear gene markers.
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Affiliation(s)
- Anchittha Satjarak
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln drive, Madison, Wisconsin, USA
| | - John A Burns
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York, USA
| | - Eunsoo Kim
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York, USA
| | - Linda E Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln drive, Madison, Wisconsin, USA
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Yurina NP, Odintsova MS. Mitochondrial Genome Structure of Photosynthetic Eukaryotes. BIOCHEMISTRY (MOSCOW) 2017; 81:101-13. [PMID: 27260390 DOI: 10.1134/s0006297916020048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Current ideas of plant mitochondrial genome organization are presented. Data on the size and structural organization of mtDNA, gene content, and peculiarities are summarized. Special emphasis is given to characteristic features of the mitochondrial genomes of land plants and photosynthetic algae that distinguish them from the mitochondrial genomes of other eukaryotes. The data published before the end of 2014 are reviewed.
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Affiliation(s)
- N P Yurina
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia.
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Farwagi AA, Fučíková K, McManus HA. Phylogenetic patterns of gene rearrangements in four mitochondrial genomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae). BMC Genomics 2015; 16:826. [PMID: 26486870 PMCID: PMC4618342 DOI: 10.1186/s12864-015-2056-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/10/2015] [Indexed: 11/16/2022] Open
Abstract
Background The variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale. Sequenced mt genomes from the chlorophycean orders Volvocales and Sphaeropleales exhibit considerable variation in size, content, and structure, even among closely related genera. However, sampling of mt genomes on a within-family scale is still poor and the sparsity of information precludes a thorough understanding of genome evolution in the green algae. Methods Genomic DNA of representative taxa were sequenced on an Illumina HiSeq2500 to produce 2x100 bp paired reads, and mitochondrial genomes were assembled and annotated using Geneious v.6.1.5. Phylogenetic analysis of 13 protein-coding mitochondrial genes spanning the Sphaeropleales was performed. Results This study presents one of the first within-family comparisons of mt genome diversity, and is the first to report complete mt genomes for the family Hydrodictyaceae (order Sphaeropleales). Four complete mt genomes representing three taxa and four phylogenetic groups, Stauridium tetras, Pseudopediastrum boryanum, and Pediastrum duplex, range in size from 37,723 to 53,560 bp. The size variability is primarily due to intergenic region expansion, and intron content is generally low compared with other mt genomes of Sphaeropleales. Conclusions Certain gene rearrangements appear to follow a phylogenetic pattern, and with a more thorough taxon sampling genome-level sequence may be useful in resolving systematic conundrums that plague this morphologically diverse family. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2056-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Audrey A Farwagi
- Department of Biological Sciences, Le Moyne College, Syracuse, NY, USA.
| | - Karolina Fučíková
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.
| | - Hilary A McManus
- Department of Biological Sciences, Le Moyne College, Syracuse, NY, USA.
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Melton JT, Leliaert F, Tronholm A, Lopez-Bautista JM. The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta). PLoS One 2015; 10:e0121020. [PMID: 25849557 PMCID: PMC4388391 DOI: 10.1371/journal.pone.0121020] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4), atp1 (1), nad3 (1), nad5 (1), and rrs (3). Double-cut-and-join (DCJ) values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta). A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales) and Tetraselmis (Chlorodendrophyceae) closely to Ulva (Ulvales) and Pseudendoclonium (Ulothrichales).
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Affiliation(s)
- James T. Melton
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
- * E-mail:
| | - Frederik Leliaert
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Ana Tronholm
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949, United States of America
| | - Juan M. Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
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Nishimura Y, Kamikawa R, Hashimoto T, Inagaki Y. An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333. Mob Genet Elements 2014; 4:e29384. [PMID: 25054084 PMCID: PMC4091101 DOI: 10.4161/mge.29384] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/27/2014] [Accepted: 05/27/2014] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames.
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Affiliation(s)
- Yuki Nishimura
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan ; Graduate School of Systems and Information Engineering; University of Tsukuba; Tsukuba, Japan
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies; Kyoto University; Kyoto, Japan ; Graduate School of Global Environmental Studies; Kyoto University; Kyoto, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan ; Center for Computational Sciences; University of Tsukuba; Tsukuba, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan ; Center for Computational Sciences; University of Tsukuba; Tsukuba, Japan
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Turmel M, Otis C, Lemieux C. Tracing the evolution of streptophyte algae and their mitochondrial genome. Genome Biol Evol 2014; 5:1817-35. [PMID: 24022472 PMCID: PMC3814193 DOI: 10.1093/gbe/evt135] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Six monophyletic groups of charophycean green algae are recognized within the Streptophyta. Although incongruent with earlier studies based on genes from three cellular compartments, chloroplast and nuclear phylogenomic analyses have resolved identical relationships among these groups, placing the Zygnematales or the Zygnematales + Coleochaetales as sister to land plants. The present investigation aimed at determining whether this consensus view is supported by the mitochondrial genome and at gaining insight into mitochondrial DNA (mtDNA) evolution within and across streptophyte algal lineages and during the transition toward the first land plants. We present here the newly sequenced mtDNAs of representatives of the Klebsormidiales (Entransia fimbriata and Klebsormidium spec.) and Zygnematales (Closterium baillyanum and Roya obtusa) and compare them with their homologs in other charophycean lineages as well as in selected embryophyte and chlorophyte lineages. Our results indicate that important changes occurred at the levels of genome size, gene order, and intron content within the Zygnematales. Although the representatives of the Klebsormidiales display more similarity in genome size and intron content, gene order seems more fluid and gene losses more frequent than in other charophycean lineages. In contrast, the two members of the Charales display an extremely conservative pattern of mtDNA evolution. Collectively, our analyses of gene order and gene content and the phylogenies we inferred from 40 mtDNA-encoded proteins failed to resolve the relationships among the Zygnematales, Coleochaetales, and Charales; however, they are consistent with previous phylogenomic studies in favoring that the morphologically complex Charales are not sister to land plants.
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Affiliation(s)
- Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, Canada
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Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol 2014; 14:23. [PMID: 24533922 PMCID: PMC3933183 DOI: 10.1186/1471-2148-14-23] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 01/13/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. RESULTS We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. CONCLUSIONS Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.
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Affiliation(s)
- Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475, USA
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Liu Y, Wang B, Cui P, Li L, Xue JY, Yu J, Qiu YL. The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants. PLoS One 2012; 7:e35168. [PMID: 22511984 PMCID: PMC3325193 DOI: 10.1371/journal.pone.0035168] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Accepted: 03/13/2012] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial genomes have maintained some bacterial features despite their residence within eukaryotic cells for approximately two billion years. One of these features is the frequent presence of polycistronic operons. In land plants, however, it has been shown that all sequenced vascular plant chondromes lack large polycistronic operons while bryophyte chondromes have many of them. In this study, we provide the completely sequenced mitochondrial genome of a lycophyte, from Huperzia squarrosa, which is a member of the sister group to all other vascular plants. The genome, at a size of 413,530 base pairs, contains 66 genes and 32 group II introns. In addition, it has 69 pseudogene fragments for 24 of the 40 protein- and rRNA-coding genes. It represents the most archaic form of mitochondrial genomes of all vascular plants. In particular, it has one large conserved gene cluster containing up to 10 ribosomal protein genes, which likely represents a polycistronic operon but has been disrupted and greatly reduced in the chondromes of other vascular plants. It also has the least rearranged gene order in comparison to the chondromes of other vascular plants. The genome is ancestral in vascular plants in several other aspects: the gene content resembling those of charophytes and most bryophytes, all introns being cis-spliced, a low level of RNA editing, and lack of foreign DNA of chloroplast or nuclear origin.
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Affiliation(s)
- Yang Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Bin Wang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peng Cui
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Libo Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jia-Yu Xue
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- School of Life Sciences, Nanjing University, Nanjing, Jiangsu, People's Republic of China
| | - Jun Yu
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yin-Long Qiu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Liu Y, Xue JY, Wang B, Li L, Qiu YL. The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: dynamic and conservative evolution. PLoS One 2011; 6:e25836. [PMID: 21998706 PMCID: PMC3187804 DOI: 10.1371/journal.pone.0025836] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/12/2011] [Indexed: 11/19/2022] Open
Abstract
Early land plant mitochondrial genomes captured important changes of mitochondrial genome evolution when plants colonized land. The chondromes of seed plants show several derived characteristics, e.g., large genome size variation, rapid intra-genomic rearrangement, abundant introns, and highly variable levels of RNA editing. On the other hand, the chondromes of charophytic algae are still largely ancestral in these aspects, resembling those of early eukaryotes. When the transition happened has been a long-standing question in studies of mitochondrial genome evolution. Here we report complete mitochondrial genome sequences from an early-diverging liverwort, Treubia lacunosa, and a late-evolving moss, Anomodon rugelii. The two genomes, 151,983 and 104,239 base pairs in size respectively, contain standard sets of protein coding genes for respiration and protein synthesis, as well as nearly full sets of rRNA and tRNA genes found in the chondromes of the liverworts Marchantia polymorpha and Pleurozia purpurea and the moss Physcomitrella patens. The gene orders of these two chondromes are identical to those of the other liverworts and moss. Their intron contents, with all cis-spliced group I or group II introns, are also similar to those in the previously sequenced liverwort and moss chondromes. These five chondromes plus the two from the hornworts Phaeoceros laevis and Megaceros aenigmaticus for the first time allowed comprehensive comparative analyses of structure and organization of mitochondrial genomes both within and across the three major lineages of bryophytes. These analyses led to the conclusion that the mitochondrial genome experienced dynamic evolution in genome size, gene content, intron acquisition, gene order, and RNA editing during the origins of land plants and their major clades. However, evolution of this organellar genome has remained rather conservative since the origin and initial radiation of early land plants, except within vascular plants.
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Affiliation(s)
- Yang Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jia-Yu Xue
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- School of Life Sciences, Nanjing University, Nanjing, Jiangsu, People’s Republic of China
| | - Bin Wang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Libo Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yin-Long Qiu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Leliaert F, Verbruggen H, Zechman FW. Into the deep: New discoveries at the base of the green plant phylogeny. Bioessays 2011; 33:683-92. [PMID: 21744372 DOI: 10.1002/bies.201100035] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Frederik Leliaert
- Biology Department, Phycology Research Group, Ghent University, Ghent, Belgium.
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Tsunewaki K. Interorganellar DNA transfer in wheat: dynamics and phylogenetic origin. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2011; 87:529-49. [PMID: 21986316 PMCID: PMC3313693 DOI: 10.2183/pjab.87.529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/01/2011] [Indexed: 05/31/2023]
Abstract
A homology search of wheat chloroplast (ct) and mitochondrial (mt) genomes identified 54 ctDNA segments that have homology with 66 mtDNA segments. The mtDNA segments were classified according to their origin: orthologs (prokaryotic origin), xenologs (interorganellar DNA transfer origin) and paralogs (intraorganellar DNA amplification origin). The 66 mtDNA sequences with homology to ctDNA segments included 14 paralogs, 18 orthologs and 34 xenologs. Analysis of the xenologs indicated that the DNA transfer occurred unidirectionally from the ct genome to the mt genome. The evolutionary timing of each interorganellar DNA transfer that generated a xenolog was estimated. This analysis showed that 2 xenologs originated early in green plant evolution, 4 in angiosperm evolution, 3 in monocotyledon evolution, 9 during cereal diversification and 8 in the evolution of wheat. Six other xenologs showed recurrent transfer from the ct to mt genomes in more than one taxon. The two remaining xenologs were uninformative on the evolutionary timing of their transfer. The wheat mt nad9 gene was found to be chimeric, consisting of the cereal nad9 gene and its 291 bp 5'-flanking region that included a 58 bp xenolog of the ct-ndhC origin.
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Popper ZA, Michel G, Hervé C, Domozych DS, Willats WGT, Tuohy MG, Kloareg B, Stengel DB. Evolution and diversity of plant cell walls: from algae to flowering plants. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:567-90. [PMID: 21351878 DOI: 10.1146/annurev-arplant-042110-103809] [Citation(s) in RCA: 409] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) endosymbiotic events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence.
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Affiliation(s)
- Zoë A Popper
- Botany and Plant Science, School of Natural Sciences, National University of Ireland, Galway, Ireland
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Regina TMR, Quagliariello C. Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2010; 48:646-54. [PMID: 20605476 DOI: 10.1016/j.plaphy.2010.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 04/26/2010] [Accepted: 05/04/2010] [Indexed: 05/04/2023]
Abstract
According to PCR assays and sequencing, we now report the shared presence of two rps3 introns, namely the rps3i74 and the rps3i249, in the mitochondria of all the classes representing the surviving lineages of gymnosperms, and unveil several lineages experiencing intron loss. Interestingly, the rps3 intron gains and losses within the four groups of gymnosperms let us sort out the Pinaceae and the non-Pinaceae into intron (+)- and intron (-)-lineages, respectively. Worthy of mention is also the finding that only Gnetum within the Gnetales harbours both the rps3 introns. This intron distribution pattern is consistent with the hypothesis that the two rps3 introns were likely present in the common ancestor of the seed plants and, then, independently lost in the non-Pinaceae during gymnosperm evolution. The derived secondary structural model of the novel group IIA intron improves our understanding of the significance and origin of the extraordinary length polymorphisms observed among rps3i249 orthologs. Despite the remarkable structural plasticity to adopt and reject introns, the rps3 mRNAs undergo accurate processing by splicing and extensive editing in gymnosperm mitochondria. This study provides additional insights into the evolutionarily high dynamics of mitochondrial introns which may come and go in closely related plant species. The turnover of the mitochondrial rps3 group II introns seen among lineages of seed plants further suggests that these introns might be an additional signature to discriminate between particularly cryptical taxonomic groups for which there is a need of a further evaluation of their evolutionary affiliation.
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Affiliation(s)
- Teresa M R Regina
- Dipartimento di Biologia Cellulare, Università degli Studi della Calabria, Ponte P. Bucci, 87030 Arcavacata di Rende, Italy
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Timme RE, Delwiche CF. Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes. BMC PLANT BIOLOGY 2010; 10:96. [PMID: 20500869 PMCID: PMC2890016 DOI: 10.1186/1471-2229-10-96] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 05/25/2010] [Indexed: 05/19/2023]
Abstract
UNLABELLED The large and diverse land plant lineage is nested within a clade of fresh water green algae, the charophytes. Collection of genome-scale data for land plants and other organisms over the past decade has invigorated the field of evolutionary biology. One of the core questions in the field asks: how did a colonization event by a green algae over 450 mya lead to one of the most successful lineages on the tree of life? This question can best be answered using the comparative method, the first step of which is to gather genome-scale data across closely related lineages to land plants. Before sequencing an entire genome it is useful to first gather transcriptome data: it is less expensive, it targets the protein coding regions of the genome, and provides support for gene models for future genome sequencing. We built Expressed Sequence Tag (EST) libraries for two charophyte species, Coleochaete orbicularis (Coleochaetales) and Spirogyra pratensis (Zygnematales). We used both Sanger sequencing and next generation 454 sequencing to cover as much of the transcriptome as possible. RESULTS Our sequencing effort for Spirogyra pratensis yielded 9,984 5' Sanger reads plus 598,460 GS FLX Standard 454 sequences; Coleochaete orbicularis yielded 4,992 5' Sanger reads plus 673,811 GS FLX Titanium 454 sequences. After clustering S. pratensis yielded 12,000 unique transcripts, or unigenes, and C. orbicularis yielded 19,000. Both transcriptomes were very plant-like, i.e. most of the transcripts were more similar to streptophytes (land plants + charophyte green algae) than to other green algae in the sister group chlorophytes. BLAST results of several land plant genes hypothesized to be important in early land plant evolution resulted in high quality hits in both transcriptomes revealing putative orthologs ripe for follow-up studies. CONCLUSIONS Two main conclusions were drawn from this study. One illustrates the utility of next generation sequencing for transcriptome studies: larger scale data collection at a lower cost enabled us to cover a considerable portion of the transcriptome for both species. And, two, that the charophyte green algal transcriptoms are remarkably plant-like, which gives them the unique capacity to be major players for future evolutionary genomic studies addressing origin of land plant questions.
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Affiliation(s)
- Ruth E Timme
- Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Charles F Delwiche
- Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
- Cell Biology and Molecular Genetics, Maryland Agricultural Experiment Station, University of Maryland, College Park, College Park, MD 20742, USA
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A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga Pycnococcus provasolii. J Mol Evol 2010; 70:203-14. [PMID: 20135105 DOI: 10.1007/s00239-010-9322-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
Abstract
Reduction in size of flagellated chlorophytes occurred multiple times during evolution, providing the opportunity to study the consequences of cell reduction on genome architecture. Recent investigations on the chloroplast genomes of the tiny prasinophyceans Ostreococcus tauri (Mamiellales), Micromonas sp. RCC299 (Mamiellales), and Pycnococcus provasolii (Pseudocourfieldiales) highlighted their extreme compaction and reduced gene repertoires. Genome compaction is also exemplified by the Ostreococcus and Micromonas mitochondrial DNAs (mtDNAs) although they have retained almost all of the about 65 genes presumably present in the mitochondria of ancestral prasinophyceans. In this study, the mitochondrial genome of Pycnococcus was sequenced and compared to those of previously examined chlorophytes. Our results document the first case where cellular reduction of a free-living alga was accompanied by marked reduction in gene content of both the mitochondrial and chloroplast genomes. At 24,321 bp, the intronless Pycnococcus mitochondrial genome falls within the lower size range displayed by green algal mtDNAs. The 36 conserved genes, specifying two rRNAs with conventional structures, 16 tRNAs and 18 proteins, are all encoded on the same DNA strand and represent 88% of the genome. Besides a pronounced codon bias, the protein-coding genes feature a variant genetic code characterized by the use of TGA (normally a stop codon) to code for tryptophan, and the unprecedented use of TTA and TTG (normally leucine codons) as stop codons. We conclude that substantial reduction of the mitochondrial genome occurred in at least three independent chlorophyte lineages and that this process entailed a number of convergent changes in these lineages.
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Borza T, Redmond EK, Laflamme M, Lee RW. MITOCHONDRIAL DNA IN THE OOGAMOCHLAMYS CLADE (CHLOROPHYCEAE): HIGH GC CONTENT AND UNIQUE GENOME ARCHITECTURE FOR GREEN ALGAE(1). JOURNAL OF PHYCOLOGY 2009; 45:1323-34. [PMID: 27032590 DOI: 10.1111/j.1529-8817.2009.00753.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Most mitochondrial genomes in the green algal phylum Chlorophyta are AT-rich, circular-mapping DNA molecules. However, mitochondrial genomes from the Reinhardtii clade of the Chlorophyceae lineage are linear and sometimes fragmented into subgenomic forms. Moreover, Polytomella capuana, from the Reinhardtii clade, has an elevated GC content (57.2%). In the present study, we examined mitochondrial genome conformation and GC bias in the Oogamochlamys clade of the Chlorophyceae, which phylogenetic data suggest is closely related to the Reinhardtii clade. Total DNA from selected Oogamochlamys taxa, including four Lobochlamys culleus (H. Ettl) Pröschold, B. Marin, U. G. Schlöss. et Melkonian strains, Lobochlamys segnis (H. Ettl) Pröschold, B. Marin, U. G. Schlöss. et Melkonian, and Oogamochlamys gigantea (O. Dill) Pröschold, B. Marin, U. G. Schlöss. et Melkonian, was subjected to Southern blot analyses with cob and cox1 probes, and the results suggest that the mitochondrial genome of these taxa is represented by multiple-sized linear DNA fragments with overlapping homologies. On the basis of these data, we propose that linear mitochondrial DNA with a propensity to become fragmented arose in an ancestor common to the Reinhardtii and Oogamochlamys clades or even earlier in the evolutionary history of the Chlorophyceae. Analyses of partial cob and cox1 sequences from these Oogamochlamys taxa revealed an unusually high GC content (49.9%-65.1%) and provided evidence for the accumulation of cob and cox1 pseudogenes and truncated sequences in the mitochondrial genome of all L. culleus strains examined.
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Affiliation(s)
- Tudor Borza
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
| | - Erin K Redmond
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
| | - Mark Laflamme
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
| | - Robert W Lee
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
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Mower JP, Bonen L. Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae. BMC Evol Biol 2009; 9:265. [PMID: 19917118 PMCID: PMC2780418 DOI: 10.1186/1471-2148-9-265] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 11/16/2009] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial genomes of plants generally encode 30-40 identified protein-coding genes and a large number of lineage-specific ORFs. The lack of wide conservation for most ORFs suggests they are unlikely to be functional. However, an ORF, termed orf-bryo1, was recently found to be conserved among bryophytes suggesting that it might indeed encode a functional mitochondrial protein. Results From a broad survey of land plants, we have found that the orf-bryo1 gene is also conserved in the mitochondria of vascular plants and charophycean green algae. This gene is actively transcribed and RNA edited in many flowering plants. Comparative sequence analysis and distribution of editing suggests that it encodes ribosomal protein L10 of the large subunit of the ribosome. In several lineages, such as crucifers and grasses, where the rpl10 gene has been lost from the mitochondrion, we suggest that a copy of the nucleus-encoded chloroplast-derived rpl10 gene may serve as a functional replacement. Conclusion Despite the fact that there are now over 20 mitochondrial genome sequences for land plants and green algae, this gene has remained unidentified and largely undetected until now because of the unlikely coincidence that most of the earlier sequences were from the few lineages that lack the intact gene. These results illustrate the power of comparative sequencing to identify novel genomic features.
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Affiliation(s)
- Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Center for Plant Science Innovation, Lincoln, NE, USA.
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The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. J Mol Evol 2009; 68:665-78. [PMID: 19475442 DOI: 10.1007/s00239-009-9240-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 04/03/2009] [Accepted: 04/15/2009] [Indexed: 10/20/2022]
Abstract
Land plants possess some of the most unusual mitochondrial genomes among eukaryotes. However, in early land plants these genomes resemble those of green and red algae or early eukaryotes. The question of when during land plant evolution the dramatic change in mtDNAs occurred remains unanswered. Here we report the first completely sequenced mitochondrial genome of the hornwort, Megaceros aenigmaticus, a member of the sister group of vascular plants. It is a circular molecule of 184,908 base pairs, with 32 protein genes, 3 rRNA genes, 17 tRNA genes, and 30 group II introns. The genome contains many genes arranged in the same order as in those of a liverwort, a moss, several green and red algae, and Reclinomonas americana, an early-branching eukaryote with the most ancestral form of mtDNA. In particular, the gene order between mtDNAs of the hornwort and Physcomitrella patens (moss) differs by only 8 inversions and translocations. However, the hornwort mtDNA possesses 4 derived features relative to green alga mtDNAs--increased genome size, RNA editing, intron gains, and gene losses--which were all likely acquired during the origin and early evolution of land plants. Overall, this genome and those of other 2 bryophytes show that mitochondrial genomes in early land plants, unlike their seed plant counterparts, exhibit a mixed mode of conservative yet dynamic evolution.
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Lang D, Zimmer AD, Rensing SA, Reski R. Exploring plant biodiversity: the Physcomitrella genome and beyond. TRENDS IN PLANT SCIENCE 2008; 13:542-9. [PMID: 18762443 DOI: 10.1016/j.tplants.2008.07.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 07/24/2008] [Accepted: 07/25/2008] [Indexed: 05/18/2023]
Abstract
For decades, plant molecular biology has focused on only a few angiosperm species. Recently, the approximately 500mega base pairs (Mb) of the haploid Physcomitrella patens genome were sequenced and annotated. Mosses such as P. patens occupy a key evolutionary position halfway between green algae and flowering plants. This draft genome, in comparison to existing genome data from other plants, allows evolutionary insights into the conquest of land by plants and the molecular biodiversity that land plants exhibit. As a model organism, P. patens provides a well-developed molecular toolbox, including efficient gene targeting in combination with the morphologically simple moss tissues. We describe current as well as future tools for P. patens research and the prospects they offer for plant research in general.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
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Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture. BMC Evol Biol 2008; 8:156. [PMID: 18495022 PMCID: PMC2412866 DOI: 10.1186/1471-2148-8-156] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 05/21/2008] [Indexed: 12/03/2022] Open
Abstract
Background The magnitude of intronic and intergenic DNA can vary substantially both within and among evolutionary lineages; however, the forces responsible for this disparity in genome compactness are conjectural. One explanation, termed the mutational-burden hypothesis, posits that genome compactness is primarily driven by two nonadaptive processes: mutation and random genetic drift – the effects of which can be discerned by measuring the nucleotide diversity at silent sites (πsilent), defined as noncoding sites and the synonymous sites of protein-coding regions. The mutational-burden hypothesis holds that πsilent is negatively correlated to genome compactness. We used the model organism Chlamydomonas reinhardtii, which has a streamlined, coding-dense mitochondrial genome and an noncompact, intron-rich nuclear genome, to investigate the mutational-burden hypothesis. For measuring πsilent we sequenced the complete mitochondrial genome and portions of 7 nuclear genes from 7 geographical isolates of C. reinhardtii. Results We found significantly more nucleotide diversity in the nuclear compartment of C. reinhardtii than in the mitochondrial compartment: net values of πsilent for the nuclear and mitochondrial genomes were 32 × 10-3 and 8.5 × 10-3, respectively; and when insertions and deletions (indels) are factored in, these values become 49 × 10-3 for the nuclear DNA and 11 × 10-3 for the mitochondrial DNA (mtDNA). Furthermore, our investigations of C. reinhardtii revealed 4 previously undiscovered mitochondrial introns, one of which contains a fragment of the large-subunit (LSU) rRNA gene and another of which is found in a region of the LSU-rRNA gene not previously reported (for any taxon) to contain introns. Conclusion At first glance our results are in opposition to the mutational-burden hypothesis: πsilent was approximately 4 times greater in the nuclear compartment of C. reinhardtii relative to the mitochondrial compartment. However, when we consider the encumbrance of noncoding DNA in each of these C. reinhardtii compartments, we conclude that introns in the mtDNA impose a greater burden than those in the nuclear DNA and suggest that the same may be true for the intergenic regions. Overall, we cannot reject the mutational-burden hypothesis and feel that more data on nucleotide diversity from green algae and other protists are needed.
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Allen JWA, Jackson AP, Rigden DJ, Willis AC, Ferguson SJ, Ginger ML. Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems? FEBS J 2008; 275:2385-402. [PMID: 18393999 DOI: 10.1111/j.1742-4658.2008.06380.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mitochondrial cytochromes c and c(1) are present in all eukaryotes that use oxygen as the terminal electron acceptor in the respiratory chain. Maturation of c-type cytochromes requires covalent attachment of the heme cofactor to the protein, and there are at least five distinct biogenesis systems that catalyze this post-translational modification in different organisms and organelles. In this study, we use biochemical data, comparative genomic and structural bioinformatics investigations to provide a holistic view of mitochondrial c-type cytochrome biogenesis and its evolution. There are three pathways for mitochondrial c-type cytochrome maturation, only one of which is present in prokaryotes. We analyze the evolutionary distribution of these biogenesis systems, which include the Ccm system (System I) and the enzyme heme lyase (System III). We conclude that heme lyase evolved once and, in many lineages, replaced the multicomponent Ccm system (present in the proto-mitochondrial endosymbiont), probably as a consequence of lateral gene transfer. We find no evidence of a System III precursor in prokaryotes, and argue that System III is incompatible with multi-heme cytochromes common to bacteria, but absent from eukaryotes. The evolution of the eukaryotic-specific protein heme lyase is strikingly unusual, given that this protein provides a function (thioether bond formation) that is also ubiquitous in prokaryotes. The absence of any known c-type cytochrome biogenesis system from the sequenced genomes of various trypanosome species indicates the presence of a third distinct mitochondrial pathway. Interestingly, this system attaches heme to mitochondrial cytochromes c that contain only one cysteine residue, rather than the usual two, within the heme-binding motif. The isolation of single-cysteine-containing mitochondrial cytochromes c from free-living kinetoplastids, Euglena and the marine flagellate Diplonema papillatum suggests that this unique form of heme attachment is restricted to, but conserved throughout, the protist phylum Euglenozoa.
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