The Viscum album Gene Space database

Abstract

The hemiparasitic flowering plant Viscum album (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant Arabidopsis thaliana. To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted. A database resulting from this project contains sequences of 39,092 different open reading frames encoding 32,064 distinct proteins. Based on ‘Benchmarking Universal Single-Copy Orthologs’ (BUSCO) analysis, the completeness of the database was estimated to be in the range of 78%. To further develop this database, we performed a transcriptome project of V. album organs harvested in summer and winter based on Illumina sequencing. Data from both sequencing strategies were combined. The new V. album Gene Space database II (VaGs II) contains 90,039 sequences and has a completeness of 93% as revealed by BUSCO analysis. Sequences from other organisms, particularly fungi, which are known to colonize mistletoe leaves, have been removed. To evaluate the quality of the new database, proteome data of a mitochondrial fraction of V. album were re-analyzed. Compared to the original evaluation published five years ago, nearly 1000 additional proteins could be identified in the mitochondrial fraction, providing new insights into the Oxidative Phosphorylation System of V. album. The VaGs II database is available at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all V. album sequences have been uploaded at the European Nucleotide Archive (ENA).

Introduction

European mistletoe (V. album) is an obligate hemiparasitic flowering plant of the order Santalales. It grows on numerous trees in Europe. The host trees provide V. album with water, nutrients and, to a certain extent, with organic compounds. At the same time, V. album performs photosynthesis and produces organic compounds itself. In contrast to most angiosperms in Central Europe, it does not discard its leaves in winter and performs photosynthesis all year. The vitality of host trees may be impaired by mistletoe settlement.

V. album is known for a very special lifestyle (see Glatzel and Geils, 2009 for review): V. album does not germinate in soil but on branches of trees where it becomes connected with the xylem of its host. To ensure spreading, the fruits of V. album ripe in winter, when other food resources are scarce for birds. The fruits are very sticky to ensure a stable attachment on branches. The seeds lack a seed coat and consist of an embryo, which can germinate from the fruit without a dormancy phase. Haustoria, which are formed first during germination, are guided via negative phototropism to the surface of the branch of the host tree. After connection with the xylem of the vascular system, the haustoria take up water, minerals and organic compounds from the host plants. Afterwards, one pair of shoot segments per year per shoot apical meristem are formed by the V. album plant. The typical ball-like shape is achieved after several years by annual realignment of the new shoots, which grow in all directions. In contrast to most other plant species the leaves of V. album do not close their stomata during water shortage, which can increase water stress of the host plant. In August/September leaves of the previous year are discarded, without recycling chlorophyll, while the new leaves formed in spring stay attached, to perform photosynthesis in the winter.

Biochemically, V. album stands out with its rich content of phenolic acids, phenylpropanoids, flavonoids, triterpenes and phytosterols (Urech and Baumgartner, 2015; Jäger et al., 2021). Furthermore, V. album produces specific proteins, the viscotoxins and mistletoe lectins, which act as a biotic defense system. The stickiness of the fruits is provided by special kinds of hemicellulose compounds (Azuma Ji et al., 2000). The development of V. album is controlled by an extraordinary distribution of phytohormones. V. album extracts have immune stimulating and cytotoxic effects, which are used in medicine (Nazaruk and Orlikowski, 2016).

At the molecular level, V. album is less well characterized. The mitochondrial and chloroplast genomes have been sequenced (Petersen et al., 2015a; Petersen et al., 2015b; Skippington et al., 2015; Skippington et al., 2017) and found to lack some of the genes normally present in these organelles, especially those encoding subunits of the mitochondrial NADH dehydrogenase complex and the homologous chloroplastidic NDH complex. The complete absence of these complexes was shown by proteomic studies (Maclean et al., 2018; Senkler et al., 2018; Schröder et al., 2020; Schröder et al., 2022a).

The genome of V. album consists of 2n=20 chromosomes and is considered to be one of the larges genomes of flowering plants (Zonneveld, 2010; Novák et al., 2020). It consists of almost 100 billion base pairs. More than 50% of the genome sequence of V. album consists of highly repetitive DNA (Novák et al., 2020). The genome sequence of V. album has not been determined to date but the partial sequence of its Gene Space has recently been presented (Schröder et al., 2022b). The GC content of the gene sequences lies at about 50%, which is exceptionally high for angiosperms.

An initial approach to analyze the V. album Gene Space was based on Single Molecule Real-Time (SMRT) sequencing (PacBio sequencing) (Schröder et al., 2022b). A database resulting from this project contains 39,092 gene sequences, from which 32,064 protein sequences were derived. The results enabled the development of a first V. album Gene Space database. The completeness of this database was estimated to be in the range of 78%. To further develop this database, a V. album transcriptome project has been carried out using the Illumina sequencing approach. Analyses were performed for V. album samples harvested in winter and summer, respectively. By combining novel and existing sequencing data, we here present a new V. album database including 90,039 sequence entries. The quality of the new database is demonstrated by re-evaluation of published V. album proteome datasets.

Materials and methods

Isolation of mRNA fractions from V. album

Mistletoes (European mistletoe; Viscum album), grown on an apple tree (Malus sp.) on the campus of Leibniz University Hannover were used as starting material. Various organs (leaves, stems, flower buds) of male and female plants were harvested in summer and in winter, shock-frozen using liquid nitrogen, and stored at –80°C until use. mRNA isolation and quality evaluation were carried out as described previously (Schröder et al., 2022b).

Sequence analysis

mRNA fractions were reverse transcribed into cDNA. The summer and winter fractions were analyzed separately using Illumina PE150 (paired-end read) sequencing. cDNA libraries containing 250~300 bp inserts were constructed and sequenced. Quantitative data as well as quality evaluation data of the libraries are given in Table 1.

Transcriptome assembly

The raw Illumina RNA-seq reads were first trimmed for low-quality and adaptor regions using Trimmomatic (Bolger et al., 2014) (version 0.36, ILLUMINACLIP : ADAPTER.fa:2:20:7 SLIDINGWINDOW:4:15 MINLEN:50). The trimmed reads were assembled using Trinity (Haas et al., 2013) (version 2.11.0) including in silico normalization with a target coverage of 50 x. The PacBio IsoSeq reads were included in the assembly using the “–long_reads” option of Trinity. The assembled transcripts were screened for coding sequences using TransDecoder (Haas and Papanicolaou, n.d.). The potential protein sequences were merged with the previously created protein sequences (Schröder et al., 2022b) and redundant sequences were filtered using CD-HIT (Li and Godzik, 2006) (version 4.7, -c 0.95 -aS 0.99). The functional annotation was computed using the best blast hit method on the UniProt/Swiss-Prot (Boutet et al., 2007) and UniProt/TrEMBL (The UniProt Consortium et al., 2023) databases. The TPM values were computed with Salmon (Patro et al., 2017) (version 1.9.0). The completeness of the filtered transcripts was estimated with BUSCO (Seppey et al., 2019) (version 5.0.0) using the viridiplantae database.

The V. album database

The final V. album Gene Space II database was created by combining PacBio and Illumina sequencing. It includes 90,039 distinct proteins. The database is accessible at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all sequences were submitted to NCBI.

Re-evaluation of the V. album mitochondria complexome

The complexome profiling approach is introduced in Schröder et al., 2022c. Primary complexome profiling data were taken from Senkler et al., 2018. Re-evaluation of the mass-spectrometry (MS) data and annotation of proteins were carried out with MaxQuant (version 2.1.4.0) using the novel VaGs II database. The settings were the same as in Senkler et al., 2018. For heatmap generation, the abundance profiles (based on iBAQ values; Schwanhäusser et al., 2011; calculated by MaxQuant) of all identified proteins were used. These profiles were aligned according to similarity by hierarchical clustering using the NOVA software (version: 0.5.8; Giese et al., 2015). The Complexome Map of the re-evaluated V. album mitochondria fractions is available at the ComplexomeMap portal at https://complexomemap.de/75.

Results and discussion

For Illumina analysis, transcripts from leaves, stems and buds of female and male V. album plants were isolated, combined and reverse-transcribed into cDNA. Organs were harvested in winter and summer and corresponding cDNA fractions were analyzed separately. Illumina sequence analysis revealed >120,000,000 reads for the summer and the winter fraction, respectively (Table 1).

Transcriptome assembly

The datasets were processed as described in the Materials and Methods section and assembled using the Trinity software package version 2.11.0 (Haas et al., 2013). The PacBio IsoSeq reads (Schröder et al., 2022b) were included to the assembly using the “–long_reads” option of Trinity. The Trinity assembly produced 650,594 transcript contigs. TransDecoder predicted potential coding sequences on 144,517 contigs. The clustering with CD-HIT produced 104,405 unique sequences, which were used for further analyses.

Functional annotation of transcripts and functional evaluation of the V. album transcript samples

Functional annotation of the 104,405 transcripts was computed using the best blast hit method on the UniProt/Swiss-Prot (Boutet et al., 2007) and UniProt/TrEMBL (The UniProt Consortium et al., 2023) databases. As a result, 51% of the sequences could be assigned a function. As expected, in most cases the greatest similarity is with sequences from the phylum Viridiplantae (green algae and the land plants). However, there are also numerous transcripts which show highest similarity to transcripts from other phyla, especially fungi. No functions could be assigned to many other sequences, which can likely be explained by the fact that no genome sequences of plants more closely related to V. album are yet available.

V. album organs used for transcript isolation were from plants living in the field. V. album leaves are known to be colonized by several endophytic fungi (Peršoh et al., 2010; Kotan et al., 2013, Ariantari et al., 2019, reviewed in Krasylenko et al., 2020). To investigate the presence of fungal sequences in our database, we evaluated the functional annotation of Illumina transcript sequences according to Phyla for the winter and summer samples (Figure 1). 37.614 of the V. album transcripts assigned to Viridiplantae. 91% of them (34.159 transcripts) likewise were present in both, the winter and the summer sample. Furthermore, 11.830 transcripts of our V. album samples were assigned to the fungi Phylum (Figure 1). Almost all fungal sequences are from the winter sample, which is probably due to the increased age of the mistletoe leaves (new leaves appear in the spring and are kept in the winter). Only 11% of the fungal sequences occur likewise in the summer and winter samples. Few of the transcripts of our V. album samples were assigned to other Phyla than Viridiplantae or fungi (Figure 1). Transcripts that could not be functionally annotated were labeled “unknown” (Figure 1). The number of transcripts of this category is similar in the winter and summer samples; also, they show quite a high intersection in terms of their occurrence in the two seasons (76%), similar to the transcripts assigned to Viridiplantae. We conclude that these sequences should be predominantly V. album transcripts. The relatively high proportion of transcripts of unknown function likely is due to the lack of comparative sequences from related plant species, but also due to the fact that V. album has a special way of life, which requires numerous proteins that do not occur in other phyla.

Figure 1

Hulsen et al., 2008).

To further analyze the origin of sequences in our V. album samples, we quantified all transcripts identified by our Illumina sequencing approach according to their assignment to Phyla (Figure 2). Transcripts per million (TPM) values of transcripts in the summer and winter samples were examined separately. As expected, TMP values are highest for transcripts assigned to Viridiplantae and clearly lower in those assigned to the fungi Phylum. This is particularly visible in the sample harvested in summer. TMP values of unassigned transcripts more resemble the values obtained for transcripts assigned to Viridiplantae, which is especially evident in the summer sample. This reconfirms that the transcripts in this category are derived from V. album rather than from fungi colonizing V. album. The absolute summed up TPM values (summer and winter sample combined) for the four categories are 1,096,579 for Viridiplantae (73%), 385,858 for “unknown” (25%), 11,497 for fungi (0.8%) and 17,789 for “others” (1.1%). Thus, about 1% of the transcripts of our V. album fractions can be classified as fungal. This should realistically reflect the conditions in the “ecological niche” V. album.

Figure 2

Nolte et al., 2018).

The Viscum album Gene Space database II

The previous V. album Gene Space database, which was created based on Single Molecule Real-Time (SMRT) sequencing (PacBio sequencing), includes 39,092 entries encoding 32,064 distinct proteins (Schröder et al., 2022b). We now designate this database VaGs I. BUSCO analyses had revealed a completeness of about 78%. Through implementation of the new Illumina sequencing data and improved transcript annotation, we hereby present a novel V. album Gene Space database, VaGs II. We decided to remove transcripts that are unambiguously assigned to the Phyla Fungi, Animals, Bacteria and Viruses based on sequence comparisons. VaGs II includes all transcripts assigned to the categories “Viridiplantae” and “unknown”. The totel number of distinct transcripts is 90,039. The BUSCO score of VaGs II is 93% (91% complete, 2% fragmented; Figure 3).

Figure 3

Schröder et al., 2022b) and the new VaGs II database as revealed by ‘Benchmarking Universal Single Copy Orthologs’ (BUSCO) analysis (Seppey et al., 2019).

A database has been developed that allows all sequences to be viewed (Figure 4). Sequences can be downloaded, proteins can be searched by ID, name, and sequence, and instructions for BLAST searches are given. Furthermore, all V. album transcript have been uploaded at the European Nucleotide Archive (ENA) (https://www.ebi.ac.uk/ena/browser/home).

Figure 4

Re-evaluation of complexome profiling data for V. album mitochondria using VaGs II

To test the quality of the new VaGs II databank, a published proteomic dataset on V. album mitochondria (Senkler et al., 2018) was re-evaluated. This is a complexome dataset which was created as follows: First, mitochondria were isolated from V. album and a mild detergent was used to dissolve the mitochondrial membranes. Protein complexes in the resulting solution were separated by Blue-native polyacrylamide gel electrophoresis. A lane of the native gel was then cut from top to bottom into 54 small gel slices, which were individually subjected to label-free quantitative shotgun mass spectrometry for protein identifications. Finally, abundance profiles along the blue-native gel lane were calculated for all identified proteins. The results were visualized as a heatmap and the profiles of individual proteins were aligned according to similarity. On the resulting heatmap, proteins belonging to the same protein complex form characteristic clusters. It thus is possible to systematically investigate the protein complexes of a biochemical fraction, the ‘complexome’. The original data of this experiment still had to be analyzed using a protein database for the model plant Arabidopsis thaliana (Senkler et al., 2018), since a V. album database was not available. This allowed the identification of 477 proteins in total. Re-evaluation of the same dataset using the VaGs II database now allowed the identification of 1392 proteins (Figure 5). The newly evaluated mitochondrial complexome of V. album is presented as a supplement of this publication (Supplementary Table 1) and is also accessible at the ComplexomeMap portal at https://complexomemap.de/75. It offers novel insights into the molecular biology of V. album mitochondria. Also, the number of peptides identified in the complexome fractions (gel slices) significantly increased based on VaGs II evaluation, resulting in a better coverage of proteins by peptides.

Figure 5

Senkler et al., 2018. The dataset was evaluated by TAIR10 (as in Senkler et al., 2018), VaGs I (Schröder et al., 2022b) and VaGs II (this study).

To further analyze the mitochondrial complexome from V. album, as revealed by VaGs II evaluation, we took a closer look at the protein clusters corresponding to respiratory chain complexes III and IV (Figure 6). Complex III is an ubiquinol:cytochrome-c oxidoreductase and complex IV a cytochrome-c:O₂ oxidoreductase. These two protein complexes catalyze the last two steps of the mitochondrial respiratory chain and were found to form two exceptionally stable supercomplexes in V. album mitochondria (Senkler et al., 2018). According to current knowledge (Maldonado et al., 2021), complexes III and IV in plants each consist of 10 different subunits (the 10 subunits of complex III, however, all are present in duplicate, as complex III occurs as a functional dimer). In V. album, this dimer (III₂) associates with one or two copies of complex IV; the corresponding supercomplexes are designated III₂IV₁ and III₂IV₂. Of the total 20 different proteins present in these supercomplexes, all 20 proteins were found in our complexome dataset upon evaluation using VaGs II (Figure 6; compared to only 8 proteins based on the original evaluation, Senkler et al., 2018; see Supplementary Figure S1). 18 of the identified subunits form part of the two supercomplexes, whereas two (QCR6 of complex III₂ and Cox6b from complex IV) are partly detached and migrate in the low-molecular-mass region of the blue native gel, probably because they became detached during membrane solubilization. For some of the proteins, different isoforms are present in V. album (e.g. the Cox5b and the α- and β-MPP subunits, Supplementary Figures S2, S3). The summed-up abundance profiles of the subunits of complex III and of complex IV reveal that the amounts of the two supercomplexes are similar; furthermore, the stoichiometry of the two complexes within the supercomplexes is correctly revealed (Figure 6, bottom).

Figure 6

Senkler et al., 2018) upon analysis using the VaGs II database. Mitochondrial proteins were separated by Blue native (BN) PAGE and stained by Coomassie-blue (horizontal gel lane in the center of the Figure). The gel lane was dissected into 54 slices, which all were subjected to label-free quantitative shotgun mass spectrometry. Abundance profiles of individual proteins along the gel lane are visualized as a heatmap (figure part above the gel lane; the columns correspond to the 54 gel slices; the rows to the abundance profiles of individual proteins; normalized (max) abundance profiles are given; see scale to the left of the heatmap) and aligned according to similarity (using the NOVA software package version 0.5.8). Only profiles of the subunits of respiratory complexes III and IV are shown (for complete dataset see Supplementary Data S1 and ComplexomeMap at https://complexomemap.de/75). Protein identities are given to the right of the heatmap. Summed-up abundance profiles (given as ‘intensity based absolute quantification’ (iBAQ) values) of the subunits of the two protein complexes as well as assemblies of the complexes (supercomplexes III₂IV₁ and III₂IV₂) are given in the diagram (figure part below the gel lane; y-axis: iBAQ score; x-axis: gel slices 1-54). Results of the original evaluation (Senkler et al., 2018) are shown in Supplementary Figure S1).

Concluding remarks

We present here the Viscum album Gene Space database II, VaGs II. Based on our quantitative and qualitative evaluations, we assume that it covers well above 90% of the protein-coding genes of V. album. The database has been cleaned with respect to sequences from other organisms, particularly fungi that are known to colonize V. album leaves. The database contains 90,039 transcript sequences. In particular, the functional annotation of the sequences was improved. Moreover, winter and summer samples of V. album were studied separately based on Illumina sequencing. Further analysis of these data should provide insights into adaptations of V. album to different seasons. VaGs II should provide an important data background useful for further studying the molecular biology of this extraordinary plant.

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