Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae

Ly, Serigne Ndiawar; Garavito, Andréa; Block, Petra De; Asselman, Pieter; Guyeux, Christophe; Charr, Jean‐Claude; Janssens, Steven; Mouly, Arnaud; Hamon, Perla; Guyot, Romain

doi:10.1371/journal.pone.0232295

Cited by 26 publications

(45 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The task of fully resolving well-supported relationships has been relentlessly attempted by molecular systematics and sometimes even large amounts of molecular data may not suffice (Rokas & al., 2005;Rokas & Carroll, 2006). Reconstructing the deep divergence within the Spermacoce clade likewise does not seem to be a trivial task, although improved resolution might be attained with next-generation sequence data, as suggested by phylogenomic studies in Rubiaceae (e.g., Rydin & al., 2017;Ly & al., 2020). Regardless, phylogenies with unresolved or bush-like branches can sometimes harbour historical information.…”

Section: ■ Discussionmentioning

confidence: 99%

Molecular‐based phylogenetic placement and revision of Micrasepalum (Spermacoceae‐Rubiaceae)

Florentin

Salas

Janssens

et al. 2021

TAXON

View full text Add to dashboard Cite

Micrasepalum is a taxonomically and phylogenetically poorly understood genus of Rubiaceae endemic to the global biodiversity hotspot of the Caribbean islands. It has traditionally been associated with species in the Spermacoce clade, but never properly evaluated in a phylogenetic context. Also, little information about seed and fruit morphology of Micrasepalum species was provided in their original descriptions and the few subsequent taxonomic treatments. We performed a molecular phylogenetic study based on nuclear (ITS, ETS) and plastid (atpB-rbcL, petD, rps16, trnL-trnF) DNA sequence data to resolve the enigmatic taxonomic identity of Micrasepalum. Our analyses show a largely unresolved or poorly supported backbone in both the nuclear and plastid phylogenies of the Spermacoce clade, so that the sister relationship of Micrasepalum is still uncertain. Merging Micrasepalum with any lineage of the polyphyletic Borreria and Spermacoce or the phylogenetically well-defined Hexasepalum, Mitracarpus or Richardia would result in a morphologically heterogeneous collection of genera difficult to recognize within the Spermacoce clade. The unresolved relationships within the species-rich Spermacoce clade are suggestive of a rapid radiation in which Micrasepalum is one of several phylogenetically recalcitrant lineages, but that can be clearly defined morphologically. The genus is distinctive in having a caducous, 2-lobed calyx and indehiscent, one-seeded fruit. An updated identification key for all Caribbean genera of the Spermacoce clade and a full taxonomic revision of Micrasepalum are presented, including descriptions focused on reproductive characters, palynological analysis, a distribution map and new lectotypifications, as well as a new synonym for M. eritrichoides.

show abstract

Section: ■ Discussionmentioning

confidence: 99%

Molecular‐based phylogenetic placement and revision of Micrasepalum (Spermacoceae‐Rubiaceae)

Florentin

Salas

Janssens

et al. 2021

TAXON

View full text Add to dashboard Cite

show abstract

“…By using BLAST analysis with NMT proteins related to caffeine synthase sequences annotated from C. canephora 13 , 15 as queries against the C. humblotiana- annotated genome, we identified and manually inspected six C. humblotiana genes which were highly similar to these NMTs (Table 2 ; Supplementary Data S1 ; FASTA protein sequences of recovered genes). NMT genes were also searched and manually corrected in the assembled genome of Gardenia jasminoides 33 , ( Gardenia jasminoides J.Ellis) a Rubiaceae species in the sub-family Ixoroideae 34 for which only one complete gene was recovered: Gj9 , similar to GjNMT2 (Gj9A1032T108; pseudomolecule Gardenia 9). Two other genes were also located on pseudomolecule 1 (similar to GjA458T26 and GjA458T26), but precise manual annotation revealed stop codons and frameshifts for both of them.…”

Section: Resultsmentioning

confidence: 99%

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Raharimalala

Rombauts

McCarthy

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

show abstract

“…The species were collected at the secondary-growth forests on limestone karst substrates at low elevations ranging from 43-344 m asl. Ly et al (2020) cited that Rubiaceae are especially abundant in lowland humid tropical forests. They further added that this family is the most species-rich of the woody plant families.…”

Section: Diversity and Distribution Of Rubiaceae Species In Peñablanca Plsmentioning

confidence: 99%

“…Rubiaceae is the fourth largest family of Angiosperms (Robbrecht 1988; Barbhuiya et al 2014;Tobgay and Sridith 2019;Ly et al 2020;Batuyong et al 2021;Biag and Alejandro 2021) and exist as trees, shrubs, climbers, or herbs. They comprise 604 accepted genera (POWO 2021) and approximately 13,100 species (Delprete and Jardim 2012).…”

Section: Introductionmentioning

confidence: 99%

Diversity, distribution, and conservation status of Rubiaceae species in Peñablanca Protected Landscape and Seascape, Luzon, Philippines

Biag

Alejandro

2021

Biodiversitas

View full text Add to dashboard Cite

Abstract. Biag RA, Alejandro GJD. Diversity, distribution, and conservation status of Rubiaceae species in Peñablanca Protected Landscape and Seascape, Luzon, Philippines. Biodiversitas 22: 3627-3636. Peñablanca Protected Landscape and Seascape (PPLS) is the largest protected area (PA) in the province of Cagayan, Luzon, Philippines. As part of the Sierra Madre Mountain Range and being contiguous with the Northern Sierra Madre Natural Park, there is no doubt that this PA would display species endemism and richness. Hence, botanical surveys through purposive sampling in seven barangays/districts were conducted in the PPLS to determine the species diversity and distribution of Rubiaceae. This study also aims to identify the endemic species and determine their conservation status. Forty-two species of Rubiaceae belonging to 19 genera and 13 tribes were documented in the current study. The most species-rich tribes are Spermacoceae (9 sp.), followed by Psychotrieae (7 sp.), Pavetteae (6 sp.), Naucleae (5 sp.), Ixoreae (4 sp.), Aleisantheae (2 sp.), Mussaendeae (2 sp.), and Vanguerieae (2 sp.). The rest of the tribes, i.e., Augusteae, Coffeeae, Gardenieae, Knoxieae, and Morindeae, are represented by a single species. Minanga, Nabbabalayan and Sisim harbor the most species. Results show that 19 Philippine endemic species are thriving in the PPLS. Of these, four are threatened species; one is near threatened, three being least concern, two as data deficient, and the rest were not evaluated.

show abstract

Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae

Abstract: Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here:

Cited by 26 publications

References 68 publications

Molecular‐based phylogenetic placement and revision of Micrasepalum (Spermacoceae‐Rubiaceae)

Molecular‐based phylogenetic placement and revision of Micrasepalum (Spermacoceae‐Rubiaceae)

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Diversity, distribution, and conservation status of Rubiaceae species in Peñablanca Protected Landscape and Seascape, Luzon, Philippines

Contact Info

Product

Resources

About