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The 90% majority-rule consensus tree of a subclade of Ixoroideae from the tree from Bayesian analysis. This is a continuation of Ixoroideae as shown in fig. 3. Clade posterior probabilities are indicated below branches. Tribal abbreviations are shown in bold capital letters above branches of the corresponding clades. PAV, Pavetteae; OCT, Octotropideae; CRE, Cremasporeae.
Source publication
Rubiaceae are one of the largest families of plants, with ;13,000 species. In this study, we have estimated the phylogeny for 534 Rubiaceae taxa from 329 genera with up to five different chloroplast regions by Bayesian analysis. It resulted in a highly resolved tree with many strongly supported nodes. There is strong support for the three subfamili...
Contexts in source publication
Context 1
... subfamily Ixoroideae (figs. 3, 4, 7) includes two mono- generic tribes (Cremasporeae, Retiniphylleae), one represented by a single taxon (Alberteae), 12 well-supported monophyletic clades corresponding to tribes, several taxa that we refer to as the tribe Gardenieae ( fig. 4; not monophyletic), and a few taxa without tribal position (Boholia, here sequenced for the first time; Burchellia, Didymosalpinx, Gleasonia, Scyphiphora, Steenisia). A polytomy at the base of the subfamily consists of Condamineeae, Posoquerieae þ Sipaneeae þ Gleasonia, Sabi- ceeae, and a clade including the rest of the subfamily. In ...
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... Tribal abbreviations are shown in bold capital letters above branches of the corresponding clades. COF, Coffeeae; BER, Bertiereae; ALB, Alberteae; VAN, Vanguerieae; IXO, Ixoreae; RET, Retiniphylleae; MUS, Mussaendeae; SAB, Sabiceeae; SIP, Sipaneeae; POS, Posoquerieae; CON, Condamineeae. One subclade, labeled ''Ixoroideae cont.,'' is shown in fig. ...
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... in Africa but with one species (Bertiera guianensis; the types species) widespread in the New World tropics. Bertiereae and Coffeeae ( fig. 7) are strongly supported as sister taxa (1.0). In our analysis one of the species, Bertiera aetiopica (a sequence from GenBank by Dessein et al. [2001]), is found in the non- monophyletic Gardenieae (fig. 4). Excluding that sequence, the tribe Bertiereae has an estimated divergence time of 14.2 Ma ( fig. ...
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... tribe Octotropideae has an Old World distribution, with genera occurring in tropical Africa, Comoro Islands, Madagascar, Mascarenes, Rodriguez, and Indomalaya (Octo- tropis and Hypobatrum). We sampled six genera (Feretia, Fernelia, Hypobathrum, Kraussia, Pouchetia, Ramosmania), and they comprise a strongly supported Octotropideae ( fig. 4), which is sister to the tribe Cremasporeae ( fig. 7), congru- ent with earlier results ( Andreasen andBremer 1996, 2000;Davis et al. 2007). The estimated divergence time of Octotro- pideae is 16.7 Ma (fig. ...
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... cir- cumscription is not monophyletic ( Andreasen andBremer 1996, 2000;Persson 2000aPersson , 2000b). In our study, including 50 Gardenieae genera, we found very low support (0.8%) for a monophyletic tribe. The ''tribe'' is mixed among Cremaspor- eae þ Octotropideae and Pavetteae. However, there is support (1.0) for several Gardenieae groups ( fig. 4), some of which have been previously identified from molecular data as the ''Alibertia clade'' (here including Alibertia, Amaioua, Borojoa, Duroia, Genipa p.p., Glossostipula, Ibetralia, Kutchubaea, Melanopsidium, Stachyarrhena, Stenosepala;Andreasen and Bremer 1996;Andreasen 1997;Persson 2000aPersson , 2000b), the ''Randia clade'' ...
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... circumscription of Pavetteae, excluding Ixoreae, was proposed by Andreasen and Bremer (2000). No molecular analysis focusing on the tribe has yet been published. In our analysis the tribe is well supported (1.0), but relationships among taxa are not resolved or supported to the extent that there are in- dications of para/polyphyletic genera ( fig. 4). We included the following genera: Dictyandra, Pavetta, Coptosperma, Cladoceras (here sequenced for the first time), Leptactina, Robbrechtia (here sequenced for the first time), Paracephaelis (here sequenced for the first time), Rutidea, and Tarenna. The estimated divergence time of Pavetteae is 23.9 Ma ( fig. ...
Citations
... Acranthera and Coptosapelta, Rydin & al., 2009b) and the monogeneric Luculieae (Rydin & al., 2009b), both unassigned to subfamily. Cinchonoideae and Ixoroideae are sisters and this clade is in turn sister to Rubioideae (e.g., Bremer & Eriksson, 2009;. In contrast, Robbrecht & Manen (2006) proposed another subfamilial classification based on their supertree, subdividing Rubiaceae into two subfamilies, Cinchonoideae s.l. ...
... Comparison with selected previous classifications of Rubiaceae. -None of the early subfamilies of Rubiaceae as circumscribed by Bremekamp (1952Bremekamp ( , 1966 and Verdcourt (1958) based on a few cardinal characters, nor Robbrecht's (1988Robbrecht's ( , 1994 more broadly founded work based on distinct character combinations and trends, are supported by results of phylogenetic analyses based on molecular data (shown already in earlier work, e.g., by Bremer & al., 1995;Robbrecht & Manen, 2006;Bremer & Eriksson, 2009). For example, the monogeneric and monotribal Gleasonioideae, Guettardoideae, Hillioideae, Pomazotoideae, Ophiorrhizoideae, and Urophylloideae, all sensu Bremekamp (1966), are untenable, with Urophylloideae, Ophiorrhizoideae, and Pomazotoideae all nested within Rubioideae as delimited here and Gleasonioideae, Guettardoideae and Hillioideae within Dialypetalanthoideae as defined here ( Fig. 1; suppl. ...
... Although originally assigned to the Rubiaceae (Kuhlmann, 1925(Kuhlmann, , 1942, later students of its single species, Dialypetalanthus fuscescens Kuhlm., found it so morphologically unique that it was placed in its own family with highly uncertain relationship to other angiosperms (see Piesschaert & al., 1997;Vrijdaghs & al., 2022). It was mostly features of the androecium and corolla that appeared puzzling to many authors, but in-depth morphological studies by Piesschaert & al. (1997) and Vrijdaghs & al. (2022) have firmly placed D. fuscescens in Rubiaceae, which is consistent with results based on molecular data (Fay & al., 2000) although its precise position in the family as related to members of the Condamineeae was not revealed until later (Bremer & Eriksson, 2009;Kainulainen & al., 2010). The tribal name Dialypetalantheae is legitimately published (Reveal, 2012) and has priority over earlier tribe names (Condamineeae, Simireae, Hippotideae, Tammsieae, Calycophylleae), because it includes the type of a conserved family name, Dialypetalanthaceae Rizzini & Occhioni (Art. ...
The use of molecular data in phylogenetic reconstruction during more than three decades has greatly improved our understanding of the macroevolutionary history of the coffee family (Rubiaceae) and has provided a solid basis for improvement of its classification. Based on the results of 130 studies, among them most recent phylogenomic works, we present a consensus phylogeny and a robust classification of Rubiaceae that shed light on the evolutionary success of this highly diverse angiosperm family and can serve as a framework for ecological and evolutionary studies. There are more than 14,000 species and about 580 accepted genera of Rubiaceae that are assigned to 71 tribes, of which 68 are classified in two subfamilies (Dialypetalanthoideae with 38 tribes and Rubioideae with 30 tribes). Three tribes (Acranthereae, Coptosapelteae, Luculieae) remain unclassified as to subfamily. Sixty‐three of these 71 tribes are assigned to nine informal alliances (four in Rubioideae and five in Dialypetalanthoideae). These tribes are listed in alphabetical order within their respective alliances. Five tribes, one (Coussareeae) in Rubioideae and four (Airospermeae, Jackieae, Retiniphylleae, Steenisieae) in Dialypetalanthoideae, are excluded from these alliances due to unclear or conflicting phylogenetic positions. Thirty‐six tribes retain their tribal status but receive new generic limits to remedy their previous para‐ or polyphyletic nature. Twenty‐nine tribes not implemented in previous classifications have been added, of which three (Chioneae, Glionnetieae, Temnopterygeae) are newly described here. Basic information on phylogenies, distributions, former classifications, and useful references to previous works are provided for all accepted tribes, and future perspectives are discussed.
... The high diversity found in this family and its abundance and presence in all vegetation layers make Rubiaceae a good indicator in ecological and conservation studies (Delprete & Jardim 2012). Furthermore, the plants of this family have an intricate relationship with several pollinators and their fruits are a common food source for tropical fauna (Gentry & Emmons 1987;Bremer & Eriksson 2009). In Brazil, the family Rubiaceae is represented by 1,417 species within 128 genera; it occurs in every phytogeographic domain (Flora e Funga do Brasil 2023, continuously updated) and is especially diverse in the Amazon basin, Atlantic Forest, and Cerrado (Delprete & Jardim 2012). ...
We present a floristic survey of the family Rubiaceae in Juquery State Park, a conservation unit that harbors the largest Cerrado area in the metropolitan region of São Paulo and is a refuge within the Atlantic Forest domain. The work was conducted using conventional methods in plant taxonomy, including fieldwork between 2020 and 2023, a literature survey, visits to herbaria, and requests for specimen loans. Previous articles revealed the high diversity of the family in the park, but no specific treatment had been published. In the present study, 35 species distributed in 15 genera were recorded in different phytophysiognomies, and Borreria (7 spp.), Palicourea (5 spp.), Coccocypselum (4 spp.), Psychotria (4 spp.), and Galianthe (3 spp.) are the richest. Four genera (Cordiera, Hexasepalum, Malanea and Mitracarpus) and 21 species are new records for this conservation unit. A dichotomous identification key and photos of the species are also provided. The diversity of Rubiaceae species in the study area is greater than previously recorded in broader surveys, and the mosaic formed by open and forest phytophysiognomies in the park probably contributes to this high level of diversity.
... Within the Rubieae complex (here Putorieae-Rubieae-Theligoneae), Theligoneae is the sister group to Putorieae, which is concordant with previous estimates based on nuclear data [36], and with the plastome-based tree of Antonelli et al. [38] and the Sanger plastid tree of Yang et al. [92]. Plastid-based results in other studies have found Theligoneae as sister to Rubieae, i.e., the plastome trees in Wikström et al. [35] and results based on Sanger-sequenced data [34,71,[93][94][95]. It is interesting to note that the two previous phylogenomic studies that both mainly relied on CDS plastome data and have similar taxon sampling density (i.e., usually one representative per tribe) show strongly conflicting topologies. ...
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
... The phylogenetic tree generated during this research and 10 calibration constraints were used to calculate the time tree with the RelTime method [27,28]. Calibration constraints were taken from the published article [29]. The visualisation was carried out in the ape 5.7-1 and strap 1.6-0 R packages [30,31]. ...
... It was found that the genes of G. nanlingensis differ from the reference genome and mapped sequences, raising questions about the identification of this species. In addition, the divergence time tree was constructed using fossil data ( Figure S2) [29]. The estimated divergence times show connections with the RSCU values presented in Figure 5. ...
Galium genus belongs to the Rubiaceae family, which consists of approximately 14,000 species. In comparison to its well-known relatives, the plastomes of the Galium genus have not been explored so far. The plastomes of this genus have a typical, quadripartite structure, but differ in gene content, since the infA gene is missing in Galium palustre and Galium trfidum. An evaluation of the effectiveness of using entire chloroplast genome sequences as superbarcodes for accurate plant species identification revealed the high potential of this method for molecular delimitation within the genus and tribe. The trnE-UUC-psbD region showed the biggest number of diagnostides (di-agnostic nucleotides) which might be new potential barcodes, not only in Galium, but also in other closely related genera. Relative synonymous codon usage (RSCU) appeared to be connected with the phylogeny of the Rubiaceae family, showing that during evolution, plants started preferring specific codons over others.
... A widespread but predominantly tropical family present on all continents, the Rubiaceae are the fourth-largest flowering-plant family in the world (Robbrecht, 1988;Davis et al., 2009). Since the advent of molecular phylogenetic studies in the 1990s, three subfamilies have generally been accepted (Bremer & Eriksson, 2009): Rubioideae, Ixoroideae and Cinchonoideae. The Gardenieae is a tribe within the Ixoroideae, in which phylogenetic relationships are not yet fully resolved (Persson, 2000;Bremer & Eriksson, 2009;Razafimandimbison et al., 2011;Kainulainen et al., 2013;Mouly et al., 2014). ...
... Since the advent of molecular phylogenetic studies in the 1990s, three subfamilies have generally been accepted (Bremer & Eriksson, 2009): Rubioideae, Ixoroideae and Cinchonoideae. The Gardenieae is a tribe within the Ixoroideae, in which phylogenetic relationships are not yet fully resolved (Persson, 2000;Bremer & Eriksson, 2009;Razafimandimbison et al., 2011;Kainulainen et al., 2013;Mouly et al., 2014). The type genus of this tribe is Gardenia J.Ellis. ...
Identified as Gardenia over a century ago, three known species from Thailand to south China differ considerably from typical members of that genus, from which growth habits, aspects of branch architecture and corolla shape set them apart. They form a new genus, here named Thaigardenia, the species of which are scrambling to thicket-forming shrubs to sometimes treelets or small trees. They have typically unequal (asymmetric) development of each internode that offsets what began as opposite pairs of axillary buds (and potential axillary branches) from subtending leaf axils at the same level, and small infundibular corollas with insignificant tubular bases. In contrast, typical Gardenia are non-scrambling shrubs or trees, often have extra-axillary buds or branches that consistently continue to develop at the same level (i.e., remaining opposite); and showy hypocrateriform (salverform) corollas with elongate tubular bases. The unequal development of different sides of an internode that brings an initially opposite pair of axillary buds (branches) to different levels, so that they do not appear paired subsequently, is, as far as is known, unique and unknown in other Rubiaceae or opposite-leaved plants; this shared feature is a key synapomorphic character for species of the newly recognised genus.
... presents bilobed stipules, pink inflorescence and flowers, blue drupes, and adaxially concave pyrenes, thus matching the morphological circumscription of Psychotria subgenus Heteropsychotria Steyermark (1972: 484). Nevertheless, morphological and molecular studies of Psychotria Linnaeus (1759: 929) and Palicourea Aublet (1775: 172-175) have revealed that species in P. subgenus Heteropsychotria are more closely related to Palicourea than to the remaining Psychotria (Taylor 1997, Nepokroeff et al. 1999, Andersson 2002, Robbrecht & Manen 2006, Bremer & Eriksson 2009, Barrabé et al. 2012Sedio et al. 2013, Razafimandimbison et al. 2014, Taylor 2024. ...
Here we propose a lectotypification and a new name for the Brazilian Psychotria dusenii Standl. to be treated under Palicourea Aubl. The name Psychotria dusenii sensu Standley is illegitimate because it was previously assigned to an African Psychotria L. species described by K. Schumann. The new name proposed is Palicourea roseocalycina Torres-Leite.
... The tribe includes over 200 species in 12 currently recognized genera and can be divided into three main lineages (Thureborn et al., 2019) (Heads, 2017;Puff, 1986;Thureborn et al., 2019). Relaxed molecular clock analyses have provided stem age estimates of c. 43 Ma (Wikström et al., 2015(Wikström et al., , 2016 and c. 47 Ma (Bremer & Eriksson, 2009), but an ancient Gondwanan origin has also been suggested on the basis of a vicariance model (Heads, 2017). ...
Genome skimming (shallow whole‐genome sequencing) offers time‐ and cost‐efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter‐plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA – rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.
... This variation has inspired multiple studies to understand patterns of trait evolution (Bremer and Eriksson, 1992;Ferrero et al., 2012;Razafimandimbison et al., 2014;Ehrendorfer et al., 2019), and the family has been used as a model to characterize angiosperm macroevolution (Antonelli et al., 2009). While many phylogenetic studies have been performed for different clades in Rubiaceae (Löfstrand et al., 2019;Borges et al., 2021;Razafimandimbison et al., 2021;Amenu et al., 2022), as well for the entire family (Bremer and Eriksson, 2009), these have mostly relied on a few loci. Only a handful of studies have used genomic-scale phylogenetic data to resolve relationships within Rubiaceae, with most of these using the Angiosperms353 data (Antonelli et al., 2021;Canales et al., 2022;Thureborn et al., 2022) and another using microarray technology (Prata et al., 2018). ...
... Ma for Hillieae vs. 63.0 Ma for Palicoureeae +Psychotrieae (Bremer and Eriksson, 2009). By representing an older clade, Palicoureeae+Psychotrieae may have accumulated more substitutions through time. ...
... In the ASTRAL analyses of a subset of our sampled Rubiaceae, most nodes were recovered with high support (LPP ≥ 0.98) in both species trees, including relationships between closely related Palicourea species, despite only including the small proportion of loci with no paralog warnings (14%) in the analyses. Relationships between tribes and subfamilies were mostly consistent with previous studies (Bremer and Eriksson, 2009;Wikström et al., 2015). One major distinction is that our results reject the monophyly of subfamily Cinchonoideae. ...
Premise
Rubiaceae is among the most species‐rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large‐scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single‐copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae‐specific probe set that allows for comparable phylogenetic inference across clades is lacking.
Methods
Here, we use publicly accessible genomic resources to identify putatively single‐copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent‐aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.
Results
We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.
Discussion
Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.
... The family occurs on all continents, but most taxa are in tropical or subtropical areas, and the species occupy many types of habitat in different biogeographical regions. The diversity in the family is significant, with a span of lifeforms from small, weedy herbs to large rainforest trees, flower types adapted to a wide range of pollinators, different fruit types with many kinds of dispersal mechanisms, and accumulation of different chemical compounds in the plants [1,2]. The genus Alibertia belongs to the subfamily Ixoroideae, tribe Gardenieae, subdivided into two well-defined and strongly supported lineages by phylogenetic analyses. ...
Albertia edulis is known as Puruí, and its leaf tea is used in the hypoglycemic and antihypertensive treatments of the Amazon native population. This study aimed to evaluate the phytochemical composition and antioxidant properties of the Puruí pulp fruit. The hydroethanolic (LFP-E), ethyl acetate (LFP-A), and volatile concentrate (LPF-V) extracts of Puruí lyophilized fruit pulp were analyzed via LC-ISI-IT-MS, GC, and GC-MS. Moreover, total phenolic and flavonoid content (TPC and TFC) and TEAC/ABTS and DPPH assays were conducted to determine their antioxidant capacity. Compounds palmitic acid, methyl linolenate, methyl linoleate, palmitic alcohol, benzene acetaldehyde, tridecanal, and furfural were mainly identified in the LPF-V extract. Compounds caffeic and quinic acids, genipin, annonaine, 3′-7-dimethoxy-3-hydroxyflavone, 4′-hydroxy-5,7-dimethoxyflavone, 6-hydroxy-7-epigardoside methyl ester, baicalin, and phloretin-2-O-apiofuranosyl-glucopyranoside were mainly identified in the LFP-E and LFP-A extracts. For LFP-E and LFP-A extracts, TPC values were 5.75 ± 0.75 and 66.75 ± 3.1 mg GAE/g; TFC values were 1.14 ± 0.65 and 50.97 ± 1.2 mg QE/g; DPPH assay showed EC50 values of 1021.65 ± 5.9 and 133.60 ± 3.9 µg/mL; and TEAC/ABTS assay showed values of 28.36 ± 3.7 and 142.26 ± 2.2 µM TE/g. Alibertia edulis fruits are significant sources of phenolic compounds, also showing significant antioxidant capacity. The Puruí fruit seems promising for developing innovative and healthy products for the nutritional food market.
... The Rubiaceae is a plant family in the Magnoliopsida class, containing 3 subfamilies [6], more than 600 genera and 13,000 species [33]. The first genome of a Rubiaceae family plant, Coffea canephora, was published in 2014 [13]. ...
... and G. jasminoides) and Cinchonoideae (N. cadamba) [6]. Taking account that members of the same subfamily should have more shared GCFs, plants of the Ixoroideae subfamily (Coffea spp. ...
The Rubiaceae plant family, comprising 3 subfamilies and over 13,000 species, is known for producing significant bioactive compounds such as caffeine and monoterpene indole alkaloids. Despite an increase in available genomes from the Rubiaceae family over the past decade, a systematic analysis of the metabolic gene clusters (MGCs) encoded by these genomes has been lacking. In this study, we aim to identify and analyze metabolic gene clusters within complete Rubiaceae genomes through a comparative analysis of eight species. Applying two bioinformatics pipelines, we identified 2372 candidate MGCs, organized into 549 gene cluster families (GCFs). To enhance the reliability of these findings, we developed coexpression networks and conducted orthology analyses. Using genomic data from Solanum lycopersicum (Solanaceae) for comparative purposes, we provided a detailed view of predicted metabolic enzymes, pathways, and coexpression networks. We bring some examples of MGCs and GCFs involved in biological pathways of terpenes, saccharides and alkaloids. Such insights lay the groundwork for discovering new compounds and associated MGCs within the Rubiaceae family, with potential implications in developing more robust crop species and expanding the understanding of plant metabolism. This large-scale exploration also provides a new perspective on the evolution and structure-function relationship of these clusters, offering opportunities for the highly efficient utilization of these unique metabolites. The outcome of this study contributes to a broader comprehension of the biosynthetic pathways, elucidating multiple aspects of specialized metabolism and offering innovative avenues for biotechnological applications.
