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Mota APZ, Koutsovoulos GD, Perfus-Barbeoch L, Despot-Slade E, Labadie K, Aury JM, Robbe-Sermesant K, Bailly-Bechet M, Belser C, Péré A, Rancurel C, Kozlowski DK, Hassanaly-Goulamhoussen R, Da Rocha M, Noel B, Meštrović N, Wincker P, Danchin EGJ. Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats. Nat Commun 2024; 15:773. [PMID: 38316773 PMCID: PMC10844300 DOI: 10.1038/s41467-024-44914-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing in these and other Meloidogyne genomes. In addition, we find no evidence for the enzyme telomerase or for orthologs of C. elegans telomere-associated proteins, suggesting alternative lengthening of telomeres. Instead, analyzing our assembled genomes, we identify species-specific composite repeats enriched mostly at one extremity of contigs. These repeats are G-rich, oriented, and transcribed, similarly to canonical telomeric repeats. We confirm them as telomeric using fluorescent in situ hybridization. These repeats are mostly found at one single end of chromosomes in these species. The discovery of unusual and specific complex telomeric repeats opens a plethora of perspectives and highlights the evolutionary diversity of telomeres despite their central roles in senescence, aging, and chromosome integrity.
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Affiliation(s)
- Ana Paula Zotta Mota
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France.
| | - Georgios D Koutsovoulos
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Laetitia Perfus-Barbeoch
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Evelin Despot-Slade
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Robbe-Sermesant
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Marc Bailly-Bechet
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Arthur Péré
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Corinne Rancurel
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Djampa K Kozlowski
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
- Université Côte d'Azur, Center of Modeling, Simulation, and Interactions, 28 Avenue Valrose, 06000, Nice, France
| | - Rahim Hassanaly-Goulamhoussen
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Martine Da Rocha
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Nevenka Meštrović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France.
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Despot-Slade E, Širca S, Mravinac B, Castagnone-Sereno P, Plohl M, Meštrović N. Satellitome analyses in nematodes illuminate complex species history and show conserved features in satellite DNAs. BMC Biol 2022; 20:259. [PMCID: PMC9673304 DOI: 10.1186/s12915-022-01460-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Satellite DNAs (satDNAs) are tandemly repeated non-coding DNA sequences that belong to the most abundant and the fastest evolving parts of the eukaryotic genome. A satellitome represents the collection of different satDNAs in a genome. Due to extreme diversity and methodological difficulties to characterize and compare satDNA collection in complex genomes, knowledge on their putative functional constraints and capacity to participate in genome evolution remains rather elusive. SatDNA transcripts have been detected in many species, however comparative studies of satDNA transcriptome between species are extremely rare.
Results
We conducted a genome-wide survey and comparative analyses of satellitomes among different closely related Meloidogyne spp. nematodes. The evolutionary trends of satDNAs suggest that each round of proposed polyploidization in the evolutionary history is concomitant with the addition of a new set of satDNAs in the satellitome of any particular Meloidogyne species. Successive incorporation of new sets of satDNAs in the genome along the process of polyploidization supports multiple hybridization events as the main factor responsible for the formation of these species. Through comparative analyses of 83 distinct satDNAs, we found a CENP-B box-like sequence motif conserved among 11 divergent satDNAs (similarity ranges from 36 to 74%). We also found satDNAs that harbor a splice leader (SL) sequence which, in spite of overall divergence, shows conservation across species in two putative functional regions, the 25-nt SL exon and the Sm binding site. Intra- and interspecific comparative expression analyses of the complete satDNA set in the analyzed Meloidogyne species revealed transcription profiles including a subset of 14 actively transcribed satDNAs. Among those, 9 show active transcription in every species where they are found in the genome and throughout developmental stages.
Conclusions
Our results demonstrate the feasibility and power of comparative analysis of the non-coding repetitive genome for elucidation of the origin of species with a complex history. Although satDNAs generally evolve extremely quickly, the comparative analyses of 83 satDNAs detected in the analyzed Meloidogyne species revealed conserved sequence features in some satDNAs suggesting sequence evolution under selective pressure. SatDNAs that are actively transcribed in related genomes and throughout nematode development support the view that their expression is not stochastic.
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The extensive amplification of heterochromatin in Melipona bees revealed by high throughput genomic and chromosomal analysis. Chromosoma 2021; 130:251-262. [PMID: 34837120 DOI: 10.1007/s00412-021-00764-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
Satellite DNAs (satDNAs) and transposable elements (TEs) are among the main components of constitutive heterochromatin (c-heterochromatin) and are related to their functionality, dynamics, and evolution. A peculiar case regarding the quantity and distribution of c-heterochromatin is observed in the genus of bees, Melipona, with species having a low amount of heterochromatin and species with high amount occupying almost all chromosomes. By combining low-pass genome sequencing and chromosomal analysis, we characterized the satDNAs and TEs of Melipona quadrifasciata (low c-heterochromatin) and Melipona scutellaris (high low c-heterochromatin) to understand c-heterochromatin composition and evolution. We identified 15 satDNA families and 20 TEs for both species. Significant variations in the repeat landscapes were observed between the species. In M. quadrifasciata, the repetitive fraction corresponded to only 3.78% of the genome library studied, whereas in M. scutellaris, it represented 54.95%. Massive quantitative and qualitative changes contributed to the differential amplification of c-heterochromatin, mainly due to the amplification of exclusive repetitions in M. scutellaris, as the satDNA MscuSat01-195 and the TE LTR/Gypsy_1 that represent 38.20 and 14.4% of its genome, respectively. The amplification of these two repeats is evident at the chromosomal level, with observation of their occurrence on most c-heterochromatin. Moreover, we detected repeats shared between species, revealing that they experienced mainly quantitative variations and varied in the organization on chromosomes and evolutionary patterns. Together, our data allow the discussion of patterns of evolution of repetitive DNAs and c-heterochromatin that occurred in a short period of time, after separation of the Michmelia and Melipona subgenera.
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Despot-Slade E, Mravinac B, Širca S, Castagnone-Sereno P, Plohl M, Meštrović N. The Centromere Histone Is Conserved and Associated with Tandem Repeats Sharing a Conserved 19-bp Box in the Holocentromere of Meloidogyne Nematodes. Mol Biol Evol 2021; 38:1943-1965. [PMID: 33399875 PMCID: PMC8097292 DOI: 10.1093/molbev/msaa336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Although centromeres have conserved function, centromere-specific histone H3 (CenH3) and centromeric DNA evolve rapidly. The centromere drive model explains this phenomenon as a consequence of the conflict between fast-evolving DNA and CenH3, suggesting asymmetry in female meiosis as a crucial factor. We characterized evolution of the CenH3 protein in three closely related, polyploid mitotic parthenogenetic species of the Meloidogyne incognita group, and in the distantly related meiotic parthenogen Meloidogyne hapla. We identified duplication of the CenH3 gene in a putative sexual ancestral Meloidogyne. We found that one CenH3 (αCenH3) remained conserved in all extant species, including in distant Meloidogyne hapla, whereas the other evolved rapidly and under positive selection into four different CenH3 variants. This pattern of CenH3 evolution in Meloidogyne species suggests the subspecialization of CenH3s in ancestral sexual species. Immunofluorescence performed on mitotic Meloidogyne incognita revealed a dominant role of αCenH3 on its centromere, whereas the other CenH3s have lost their function in mitosis. The observed αCenH3 chromosome distribution disclosed cluster-like centromeric organization. The ChIP-Seq analysis revealed that in M. incognita αCenH3-associated DNA dominantly comprises tandem repeats, composed of divergent monomers which share a completely conserved 19-bp long box. Conserved αCenH3-associated DNA is also confirmed in the related mitotic Meloidogyne incognita group species suggesting preservation of both centromere protein and DNA constituents. We hypothesize that the absence of centromere drive in mitosis might allow for CenH3 and its associated DNA to achieve an equilibrium in which they can persist for long periods of time.
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Affiliation(s)
| | | | - Saša Širca
- Agricultural Institute Slovenia, Ljubljana, Slovenia
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Samoluk SS, Robledo G, Bertioli D, Seijo JG. Evolutionary dynamics of an at-rich satellite DNA and its contribution to karyotype differentiation in wild diploid Arachis species. Mol Genet Genomics 2016; 292:283-296. [DOI: 10.1007/s00438-016-1271-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/04/2016] [Indexed: 11/24/2022]
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Vittorazzi SE, Lourenço LB, Recco-Pimentel SM. Long-time evolution and highly dynamic satellite DNA in leptodactylid and hylodid frogs. BMC Genet 2014; 15:111. [PMID: 25316286 PMCID: PMC4201667 DOI: 10.1186/s12863-014-0111-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/06/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Satellite DNA sequences are the most abundant components of heterochromatin and are repeated in tandem hundreds to thousands of times in the genome. However, the number of repeats of a specific satellite family can vary even between the genomes of related species or populations. The PcP190 satellite DNA family was identified in the genome of the leptodactylid frog Physalaemus cuvieri, which showed to be derived most likely from the 5S rDNA in an ancestral species. In this study, we investigate the presence of the PcP190 satellite DNA in several P. cuvieri populations and in four closely related species at the chromosomal and molecular level. Furthermore, we investigate the occurrence of this satellite DNA in the genomes of P. marmoratus as well as in representative species of the leptodactylid genus Leptodactylus (L. latrans) and the hylodid family (Crossodactylus gaudichaudii), all with the aim of investigating if the PcP190 satellite DNA presents or not a restricted distribution. RESULTS The PcP190 satellite DNA was detected in all the analyzed species. Some of them exhibited particular sequence differences, allowing the identification of species-specific groups of sequences, but in other species, the sequences were more conserved. However, in a general analysis, conserved and variable domains have been recognized within the PcP190 monomer. The chromosomal analysis performed on P. cuvieri populations and closely related species revealed high variability of the satellite DNA amount and its chromosomal location, which has always been coincident with regions of centromeric/pericentromeric heterochromatin. CONCLUSION The PcP190 satellite DNA was found in representatives of two families, Leptodactylidae and Hylodidae, indicating that these sequences are widely distributed and conserved in these frogs. There is a pattern of non-random variation within the repeating units, indicating interplay between stochastic events and selective pressure along the PcP190 sequences. Karyotypic differences involving the PcP190 satellite DNA prove to be highly dynamic on the chromosomes of the Physalaemus and its differential accumulation has contributed to the differentiation process of the Z and W sex chromosomes in P. ephippifer.
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Affiliation(s)
- Stenio Eder Vittorazzi
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brazil.
| | - Luciana Bolsoni Lourenço
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brazil.
| | - Shirlei Maria Recco-Pimentel
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brazil.
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Cafasso D, Chinali G. An ancient satellite DNA has maintained repetitive units of the original structure in most species of the living fossil plant genus Zamia. Genome 2014; 57:125-35. [PMID: 24884688 DOI: 10.1139/gen-2013-0133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ZpS1 satellite DNA is specific to the genus Zamia and presents repetitive units organized as long arrays and also as very short arrays dispersed in the genome. We have characterized the structure of the ZpS1 repeats in 12 species representative of the whole geographic distribution of the genus. In most species, the clone most common sequences (cMCS) were so similar that a general most common sequence (GMCS) of the ZpS1 repetitive unit in the genus could be obtained. The few partial variations from the GMCS found in cMCS of some species correspond to variable positions present in most other species, as indicated by the clone consensus sequences (cCS). Two species have an additional species-specific variety of ZpS1 satellite. The dispersed repeats were found to contain more mutations than repeats from long arrays. Our results indicate that all or most species of Zamia inherited the ZpS1 satellite from a common ancestor in Miocene and have maintained repetitive units of the original structure till present. The features of ZpS1 satellite in the genus Zamia are poorly compatible with the model of concerted evolution, but they are perfectly consistent with a new model of satellite evolution based on experimental evidences indicating that a specific amplification-substitution repair mechanism maintains the homogeneity and stability of the repeats structure in each satellite DNA originally present in a species as long as the species exists.
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Affiliation(s)
- Donata Cafasso
- a Dipartimento di Biologia, Complesso Universitario Monte S. Angelo, Università degli Studi di Napoli "Federico II", Via Cinthia, I-80126 Napoli, Italy
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Sequence variability of the MspI satellite DNA family of the pinewood nematode Bursaphelenchus xylophilus at different geographic scales. Mol Phylogenet Evol 2013; 70:120-9. [PMID: 24076248 DOI: 10.1016/j.ympev.2013.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 12/22/2022]
Abstract
Tandemly repeated sequences known as satellite DNA (satDNA) generally exhibit complex evolutionary patterns of concerted evolution in which mutations are homogenized and fixed in a stochastic process of molecular drive. Here, the nucleotidic variability of the MspI satDNA family of the pinewood nematode Bursaphelenchus xylophilus is analyzed in order to understand the evolutionary dynamics of satDNA at the intraspecific level. A total of 425 MspI monomer units, either PCR-amplified from isolates of local (Peninsula of Setúbal, Portugal) or worldwide origin, or retrieved from the B. xylophilus genome sequence, were characterized and compared. Whatever their origin, sliding window analysis of sequence variability patterns among monomers revealed low, moderate and highly variant domains, indicating that variable levels of evolutionary constraint may act upon the entire monomers. The phylogenetic inference based on the different sets of MspI satDNA family for this species shows a broad polymorphism of the individual monomers, which were distributed into four main clusters. However, such clustering appeared independent from the geographic origin of the nematodes, and could not discriminate isolates or groups of geographically close isolates. Rather, the formation of different phylogenetic groups within this satDNA family suggests an a priori embodying of a set of diverging repeats from a common ancestor satDNA library, which have been differently amplified along the evolutionary pathway of this species. The present work improves knowledge on the evolutionary dynamics of satDNA at the intraspecific level, and provides new information on satDNA sequence variability among natural populations sampled at a local geographic scale.
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Plohl M, Petrović V, Luchetti A, Ricci A, Satović E, Passamonti M, Mantovani B. Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks. Heredity (Edinb) 2009; 104:543-51. [PMID: 19844270 DOI: 10.1038/hdy.2009.141] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The ubiquity of satellite DNA (satDNA) sequences has raised much controversy over the abundance of divergent monomer variants and the long-time nucleotide sequence stability observed for many satDNA families. In this work, we describe the satDNA BIV160, characterized in nine species of the three main bivalve clades (Protobranchia, Pteriomorphia and Heteroconchia). BIV160 monomers are similar in repeat size and nucleotide sequence to satDNAs described earlier in oysters and in the clam Donax trunculus. The broad distribution of BIV160 satDNA indicates that similar variants existed in the ancestral bivalve species that lived about 540 million years ago; this makes BIV160 the most ancient satDNA described so far. In the species examined, monomer variants are distributed in quite a complex pattern. This pattern includes (i) species characterized by a specific group of variants, (ii) species that share distinct group(s) of variants and (iii) species with both specific and shared types. The evolutionary scenario suggested by these data reconciles sequence uniformity in homogenization-maintained satDNA arrays with the genomic richness of divergent monomer variants formed by diversification of the same ancestral satDNA sequence. Diversified repeats can continue to evolve in a non-concerted manner and behave as independent amplification-contraction units in the framework of a 'library of satDNA variants' representing a permanent source of monomers that can be amplified into novel homogeneous satDNA arrays. On the whole, diversification of satDNA monomers and copy number fluctuations provide a highly dynamic genomic environment able to form and displace satDNA sequence variants rapidly in evolution.
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Affiliation(s)
- M Plohl
- Department of Molecular Biology, Ruder Bosković Institute, Zagreb, Croatia.
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Mestrović N, Plohl M, Castagnone-Sereno P. Relevance of satellite DNA genomic distribution in phylogenetic analysis: a case study with root-knot nematodes of the genus Meloidogyne. Mol Phylogenet Evol 2008; 50:204-8. [PMID: 19007896 DOI: 10.1016/j.ympev.2008.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 05/21/2008] [Accepted: 10/06/2008] [Indexed: 01/15/2023]
Affiliation(s)
- Nevenka Mestrović
- Department of Molecular Biology, Ruder Bosković Institute, Zagreb, Croatia
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Plohl M, Luchetti A, Mestrović N, Mantovani B. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 2007; 409:72-82. [PMID: 18182173 DOI: 10.1016/j.gene.2007.11.013] [Citation(s) in RCA: 230] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 11/08/2007] [Accepted: 11/20/2007] [Indexed: 12/21/2022]
Abstract
Satellite DNAs (tandemly repeated, non-coding DNA sequences) stretch over almost all native centromeres and surrounding pericentromeric heterochromatin. Once considered as inert by-products of genome dynamics in heterochromatic regions, recent studies showed that satellite DNA evolution is interplay of stochastic events and selective pressure. This points to a functional significance of satellite sequences, which in (peri)centromeres may play some fundamental functional roles. First, specific interactions with DNA-binding proteins are proposed to complement sequence-independent epigenetic processes. The second role is achieved through RNAi mechanism, in which transcripts of satellite sequences initialize heterochromatin formation. In addition, satellite DNAs in (peri)centromeric regions affect chromosomal dynamics and genome plasticity. Paradoxically, while centromeric function is conserved through eukaryotes, the profile of satellite DNAs in this region is almost always species-specific. We argue that tandem repeats may be advantageous forms of DNA sequences in (peri)centromeres due to concerted evolution, which maintains high intra-array and intrapopulation sequence homogeneity of satellite arrays, while allowing rapid changes in nucleotide sequence and/or composition of satellite repeats. This feature may be crucial for long-term stability of DNA-protein interactions in centromeric regions.
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Affiliation(s)
- Miroslav Plohl
- Department of Molecular Genetics, Ruder Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia.
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Mestrović N, Castagnone-Sereno P, Plohl M. Interplay of selective pressure and stochastic events directs evolution of the MEL172 satellite DNA library in root-knot nematodes. Mol Biol Evol 2006; 23:2316-25. [PMID: 16982821 DOI: 10.1093/molbev/msl119] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
According to the library model, related species can have in common satellite DNA (satDNA) families amplified in differing abundances, but reasons for persistence of particular sequences in the library during long periods of time are poorly understood. In this paper, we characterize 3 related satDNAs coexisting in the form of a library in mitotic parthenogenetic root-knot nematodes of the genus Meloidogyne. Due to sequence similarity and conserved monomer length of 172 bp, this group of satDNAs is named MEL172. Analysis of sequence variability patterns among monomers of the 3 MEL172 satellites revealed 2 low-variable (LV) domains highly reluctant to sequence changes, 2 moderately variable (MV) domains characterized by limited number of mutations, and 1 highly variable (HV) domain. The latter domain is prone to rapid spread and homogenization of changes. Comparison of the 3 MEL172 consensus sequences shows that the LV domains have 6% changed nucleotide positions, the MV domains have 48%, whereas 78% divergence is concentrated in the HV domain. Conserved distribution of intersatellite variability might indicate a complex pattern of interactions in heterochromatin, which limits the range and phasing of allowed changes, implying a possible selection imposed on monomer sequences. The lack of fixed species-diagnostic mutations in each of the examined MEL172 satellites suggests that they existed in unaltered form in a common ancestor of extant species. Consequently, the evolution of these satellites seems to be driven by interplay of selective constraints and stochastic events. We propose that new satellites were derived from an ancestral progenitor sequence by nonrandom accumulation of mutations due to selective pressure on particular sequence segments. In the library of particular taxa, established satellites might be subject to differential amplification at chance due to stochastic mechanisms of concerted evolution.
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Affiliation(s)
- Nevenka Mestrović
- Department of Molecular Biology, Ruder Bosković Institute, Zagreb, Croatia
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