ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

pSATdb 2.0: a database of organellar common, polymorphic, and unique microsatellites

Microsatellites, or simple sequence repeats (SSRs), are repetitive DNA sequences typically composed of 1-6 nucleotides. These repetitive sequences are found in almost all genomes, including chloroplasts and mitochondria, and are widely distributed throughout the genomes. Microsatellites are highly polymorphic, and their length may differ from species to species. Consequently, microsatellites are widely used as molecular markers and play pivotal roles in various biological research. However, comprehensive information about the length variation of microsatellites in various organellar genome sequences is not available. Therefore, to provide mined information and explore the variability in the length of microsatellites across species, we developed a comprehensive resource named pSATdb 2.0 (polymorphic microSATellites database; https://bioinfo.icgeb.res.in/psatdb/ ). This upgraded version of its predecessor pSATdb provides comprehensive information on the frequency and distribution of 348,894 microsatellites identified in organellar genome sequences. These sequences originate from 15,681 organisms spanning 3252 genera within Metazoa and Viridiplantae. Remarkably, pSATdb 2.0 is the only database that offers information on common and polymorphic microsatellites detected between organisms, along with unique microsatellites specific to each genus. Furthermore, this database features unrestricted access and includes pioneer functionalities such as Advanced Search, BLAST, and JBrowse, which facilitate user-specific microsatellite search and its visualization within the database. The pSATdb holds immense potential for the research community to support diverse studies, including genetic diversity, genetic mapping, marker-assisted selection, and comparative population investigations.

Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems, including the constituent elements within and among species. Through various efforts in genomic data archiving, integrative analysis and value-added curation, the National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), has successfully established and currently maintains a vast amount of database resources. This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts. Here, we present a comprehensive overview of central repositories dedicated to archiving, presenting, and sharing plant omics data, introduce knowledgebases focused on variants or gene-based functional insights, highlight species-specific multiple omics database resources, and briefly review the online application tools. We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-023-00134-4.

Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis

The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.

Molecular structure, comparative and phylogenetic analysis of the complete chloroplast genome sequences of weedy rye Secale cereale ssp. segetale

The complete chloroplast genome of Secale cereale ssp. segetale (Zhuk.) Roshev. (Poaceae: Triticeae) was sequenced and analyzed to better use its genetic resources to enrich rye and wheat breeding. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other complete chloroplast genomes of the five Secale species, and multigene phylogeny. As a result of the study, it was determined that the chloroplast genome is 137,042 base pair (bp) long and contains 137 genes, including 113 unique genes and 24 genes which are duplicated in the IRs. Moreover, a total of 29 SSRs were detected in the Secale cereale ssp. segetale chloroplast genome. The phylogenetic analysis showed that Secale cereale ssp. segetale appeared to share the highest degree of similarity with S. cereale and S. strictum. Intraspecific diversity has been observed between the published chloroplast genome sequences of S. cereale ssp. segetale. The genome can be accessed on GenBank with the accession number (OL688773).

Plant mitochondrial introns as genetic markers - conservation and variation

Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species' introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.

Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans

Ilyonectria destructans is a pathogenic fungus causing root rot and other symptoms on trees and many crops. This paper analyses the mitochondrial genome of I. destructans and compares it with other published Nectriaceae mitogenomes. The I. destructans mitogenome appears as a circular DNA molecule of 42,895 bp and an overall GC content of 28.23%. It contains 28 protein-coding genes (15 core protein genes and 13 free-standing ORFs), two rRNAs and 27 tRNAs. The gene content and order were found to be conserved in the mitogenome of I. destructans and other Nectriaceae, although the genome size varies because of the variation in the number and length of intergenic regions and introns. For most core protein-coding genes in Nectriaceae species, Ka/Ks < 1 indicates purifying selection. Among some Nectriaceae representatives, only the rps3 gene was found under positive selection. Phylogenetic analyses based on nucleotide sequences of 15 protein-coding genes divided 45 Hypocreales species into six major clades matching the families Bionectriaceae, Cordycipitaceae, Clavicipitaceae, Ophiocordycipitaceae, Hypocreaceae and Nectriaceae. I. destructans appeared as a sister species to unidentified Ilyonectia sp., closely related to C. ilicicola, N. cinnabarina and a clad of ten Fusarium species and G. moniliformis. The complete mitogenome of I. destructans reported in the current paper will facilitate the study of epidemiology, biology, genetic diversity of the species and the evolution of family Nectriace and the Hypocreales order.

Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species

The complete plastome sequences of six species were sequenced to better understand the evolutionary relationships and mutation patterns in the chloroplast genome of the genus Colobanthus. The length of the chloroplast genome sequences of C. acicularis, C. affinis, C. lycopodioides, C. nivicola, C. pulvinatus and C. subulatus ranged from 151,050 to 151,462 bp. The quadripartite circular structure of these genome sequences has the same overall organization and gene content with 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames. A total of 153 repeat sequences were revealed. Forward repeats were dominant, whereas complementary repeats were found only in C. pulvinatus. The mononucleotide SSRs composed of A/T units were most common, and hexanucleotide SSRs were detected least often. Eleven highly variable regions which could be utilized as potential markers for phylogeny reconstruction, species identification or phylogeography were identified within Colobanthus chloroplast genomes. Seventy-three protein-coding genes were used in phylogenetic analyses. Reconstructed phylogeny was consistent with the systematic position of the studied species, and the representatives of the same genus were grouped in one clade. All studied Colobanthus species formed a single group and C. lycopodioides was least similar to the remaining species.

Repetitive DNA profile of the amphibian mitogenome

Background

Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians.

Results

This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry.

Conclusions

Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.

rps3 as a Candidate Mitochondrial Gene for the Molecular Identification of Species from the Colletotrichum acutatum Species Complex

Colletotrichum species form one of the most economically significant groups of pathogenic fungi and lead to significant losses in the production of major crops-in particular, fruits, vegetables, ornamental plants, shrubs, and trees. Members of the genus Colletotrichum cause anthracnose disease in many plants. Due to their considerable variation, these fungi have been widely investigated in genetic studies as model organisms. Here, we report the complete mitochondrial genome sequences of four Colletotrichum species (C. fioriniae, C. lupini, C. salicis, and C. tamarilloi). The reported circular mitogenomes range from 30,020 (C. fioriniae) to 36,554 bp (C. lupini) in size and have identical sets of genes, including 15 protein-coding genes, two ribosomal RNA genes, and 29 tRNA genes. All four mitogenomes are characterized by a rather poor repetitive sequence content with only forward repeat representatives and a low number of microsatellites. The topology of the phylogenetic tree reflects the systematic positions of the studied species, with representatives of each Colletotrichum species complex gathered in one clade. A comparative analysis reveals consistency in the gene composition and order of Colletotrichum mitogenomes, although some highly divergent regions are also identified, like the rps3 gene which appears as a source of potential diagnostic markers for all studied Colletotrichum species.

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

BACKGROUND

Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA.

RESULTS

We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats.

CONCLUSIONS

ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/ . It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research.

Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.)

Quinoa has recently gained international attention because of its nutritious seeds, prompting the expansion of its cultivation into new areas in which it was not originally selected as a crop. Improving quinoa production in these areas will benefit from the introduction of advantageous traits from free-living relatives that are native to these, or similar, environments. As part of an ongoing effort to characterize the primary and secondary germplasm pools for quinoa, we report the complete mitochondrial and chloroplast genome sequences of quinoa accession PI 614886 and the identification of sequence variants in additional accessions from quinoa and related species. This is the first reported mitochondrial genome assembly in the genus Chenopodium. Inference of phylogenetic relationships among Chenopodium species based on mitochondrial and chloroplast variants supports the hypotheses that 1) the A-genome ancestor was the cytoplasmic donor in the original tetraploidization event, and 2) highland and coastal quinoas were independently domesticated.

The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species

Colobanthus apetalus is a member of the genus Colobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genus Colobanthus consists of 25 species, including Colobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome of C. apetalus. The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae and C. apetalus, and it revealed that C. apetalus and C. quitensis form a clade that is closely related to Silene species and Agrostemma githago. Moreover, the genus Silene appeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.

Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae

PREMISE OF THE STUDY

The tropical tree family Lecythidaceae has enormous ecological and economic importance in the Amazon basin. Lecythidaceae species can be difficult to identify without molecular data, however, and phylogenetic relationships within and among the most diverse genera are poorly resolved.

METHODS

To develop informative genetic markers for Lecythidaceae, we used genome skimming to de novo assemble the full plastome of the Brazil nut tree (Bertholletia excelsa) and 23 other Lecythidaceae species. Indices of nucleotide diversity and phylogenetic signal were used to identify regions suitable for genetic marker development.

RESULTS

The B. excelsa plastome contained 160,472 bp and was arranged in a quadripartite structure. Using the 24 plastome alignments, we developed primers for 10 coding and non-coding DNA regions containing exceptional nucleotide diversity and phylogenetic signal. We also developed 19 chloroplast simple sequence repeats for population-level studies.

DISCUSSION

The coding region ycf1 and the spacer rpl16-rps3 outperformed plastid DNA markers previously used for barcoding and phylogenetics. Used in a phylogenetic analysis, the matrix of 24 plastomes showed with 100% bootstrap support that Lecythis and Eschweilera are polyphyletic. The plastomes and primers presented in this study will facilitate a broad array of ecological and evolutionary studies in Lecythidaceae.

Complete mitochondrial genome sequence of the "copper moss" Mielichhoferia elongata reveals independent nad7 gene functionality loss

The mitochondrial genome of moss Mielichhoferia elongata has been sequenced and assembled with Spades genome assembler. It consists of 100,342 base pairs and has practically the same gene set and order as in other known bryophyte chondriomes. The genome contains 66 genes including three rRNAs, 24 tRNAs, and 40 conserved mitochondrial proteins genes. Unlike the majority of previously sequenced bryophyte mitogenomes, it lacks the functional nad7 gene. The phylogenetic reconstruction and scrutiny analysis of the primary structure of nad7 gene carried out in this study suggest its independent pseudogenization in different bryophyte lineages. Evaluation of the microsatellite (simple sequence repeat) content of the M. elongata mitochondrial genome indicates that it could be used as a tool in further studies as a phylogenetic marker. The strongly supported phylogenetic tree presented here, derived from 33 protein coding sequences of 40 bryophyte species, is consistent with other reconstructions based on a number of different data sets.

A conventional PCR for differentiating common taeniid species of dogs based on in silico microsatellite analysis

Canine taeniids are among the major tapeworms with remarkable medical and economic significance. Reliable diagnosis and differentiation of dog taeniids using simple and sensitive tools are of paramount importance for establishing an efficient surveillance system. Microsatellites as abundant unique tandem repeats of short DNA motifs are useful genetic markers for molecular epidemiological studies. The purpose of the present study was to find a primer pair for rapid differentiation of major tapeworms of dogs, Taenia hydatigena, T. multiceps, T. ovis and Echinococcus granulosus, by screening existing nucleotide data. All the mitochondrial genome records as well as non-coding ITS1 sequences of Taeniidae species were downloaded from Nucleotide database from NCBI. For prediction and analysis of potential loci of STR/SSR in ITS1 as well as mitochondrial regions, we used ChloroMitoSSRDB 2.0 and GMATo v1.2. software. Different tapeworm species were categorized according to different motif sequences and type and size of each microsatellite locus. Three primer sets were designed and tested for differentiating taeniid species and evaluated in a conventional PCR system. Four taeniid species were successfully differentiated using a primer pair in a simple conventional PCR system. We predicted 2-19 and 1-4 microsatellite loci in ITS1 and mitochondrial genome, respectively. In ITS1, 41 Di and 21 Tri motifs were found in the taeniids while the majority of the motifs in the mitochondrial genome were Tetra (89) and Tri (70). It is documented that the number and diversity of microsatellite loci is higher in nuclear ITS1 region than mostly coding mitochondrial genome.

The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)

PREMISE OF THE STUDY

The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome.

METHODS AND RESULTS

A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes.

CONCLUSIONS

This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.

The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)

PREMISE OF THE STUDY

The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome.

METHODS AND RESULTS

A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes.

CONCLUSIONS

This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.

PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers

Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intra-generic differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www.bioinfocabd.upo.es/plantssr.

Towards understanding the evolution and functional diversification of DNA-containing plant organelles

Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires – which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA).