Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data; implications for the size,morphology, distribution and evolutionary history of Coffea

Morphological and molecular phylogenetic studies show that there is a close relationship between Coffea and Psilanthus. In this study we reassess species relationships based on improved species sampling for Psilanthus, including P. melanocarpus, a species that shares morpho‐taxonomic characters of both genera. Analyses are performed using parsimony and Bayesian inference, on sequence data from four plastid regions [trnL–F intron, trnL–F IGS, rpl16 intron and accD–psa1 intergenic spacer (IGS)] and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (ITS 1/5.8S/ITS 2). Several major lineages with geographical coherence, as identified in previous studies based on smaller and larger data sets, are supported. Our results also confirm previous studies showing that the level of sequence divergence between Coffea and Psilanthus species is negligible, particularly given the much longer branch lengths separating other genera of tribe Coffeeae. There are strong indications that neither Psilanthus nor Coffea is monophyletic. Psilanthus melanocarpus is nested with the Coffea–Psilanthus clade, which means that there is only one critical difference between Coffea and Psilanthus; the former has a long‐emergent style and the latter a short, included style. Based on these new data, in addition to other systematically informative evidence from a broad range of studies, and especially morphology, Psilanthus is subsumed into Coffea. This decision increases the number of species in Coffea from 104 to 124, extends the distribution to tropical Asia and Australasia and broadens the morphological characterization of the genus. The implications for understanding the evolutionary history of Coffea are discussed. A group of closely related species is informally named the ‘Coffea liberica alliance’. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 357–377.     

Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA

 Phylogenetic relationships of Coffea species were estimated from the sequences of the internal transcribed spacer (ITS 2) region of nuclear ribosomal DNA. The ITS 2 region of 37 accessions belonging to 26 Coffea taxa and to three Psilanthus species was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The level of variation was high enough to make the ITS 2 a useful tool for phylogenetic reconstruction. However, an unusual level of intraspecific variation was observed leading to some difficulty in interpreting rDNA sequence divergences. Sequences were analysed using Wagner parsimony as well as the neighbour-joining distance method. Coffea taxa were divided into several major groups which present a strong geographical correspondence (i.e. Madagascar, East Africa, Central Africa and West Africa). This organisation is well supported by cytogenetic evidence. On the other hand, the results were in contradiction with the present classification of coffee-tree taxa into two genera, namely Coffea and Psilanthus. Furthermore, additivity of parental rDNA types was not observed in the allotetraploid species C. arabica. Received: 25 July 1996 / Accepted: 18 October 1996     

Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L.

CpDNA variation among 52 tree samples belonging to 25 different taxa of Coffea and two species of Psilanthus was assessed by RFLP analysis on both the total chloroplast genome and the atpB-rbcL intergenic region. Twelve variable characters were distinguished allowing the identification of 12 different plastomes. The low sequence divergence observed might suggest that Coffea is a young genus. The results were in contradiction with the present classification into two genera. Additionally, cpDNA inheritance was studied in interspecific hybrids between C. arabica and C. canephora, and in an intraspecific progeny of C. canephora, using PCR-based markers. Both studies showed exclusively maternal inheritance of cpDNA.     

Cytogenetic and flow cytometry data expand knowledge of genome evolution in three <Emphasis Type="Italic">Coffea</Emphasis> species

Karyotype and nuclear 2C-value data are considered important in taxonomic and evolutionary approaches in Coffea. Still, new methods are needed to further support such studies, especially to determine the progenitors of Coffea arabica. In this work, new cytogenetic and flow cytometry data were used to compare Coffea arabica, Coffea canephora and Coffea congensis. These data corroborate the hypothesis that C. canephora and C. congensis originated from a single ancestor, whose basic chromosome number was x = 11. In agreement with the observations of other authors, the karyotype and mean 2C-values confirm that C. arabica is a true allotetraploid originating from two diploid Coffea species with similar genomes. Although C. canephora and C. congensis have been considered potential progenitors of C. arabica, karyotype comparison revealed that only one of these species may be parental to C. arabica. These accurate cytogenetic and flow cytometry data contribute to expand our knowledge of the Coffea genome, as well as of possible progenitors of C. arabica.     

Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome

The complete sequence of Vitis vinifera revealed that the rosid clade derives from a hexaploid ancestor. At present, no analysis of complete genome sequence is available for an asterid, the other large eudicot clade, which includes the economically important species potato, tomato and coffee. To elucidate the genomic history of asterids, we compared the sequence of an 800 kb region of diploid Coffea genome to the orthologous regions of V. vinifera, Populus trichocarpa and Arabidopsis thaliana. We found a very high level of collinearity between around 80 genes of the three rosid species and Coffea. Collinearity comparisons between orthologous and paralogous regions indicates that (1) the Coffea (and consequently all asterids) and rosids share the same hexaploid ancestor; (2) the diploidization process (loss of duplicated and redundant copies from the whole genome duplication) was very advanced in the most recent common ancestor of rosids and asterids. Finally, no additional polyploidization events were detected in the Coffea lineage. Differences in gene loss rates were detected among the three rosid species and linked to the divergence in protein sequences.     

A revision of the genus Sclerosperma (Arecaceae)

Summary  A taxonomic revision of the palm genus Sclerosperma (Arecaceae) is presented. Three species are recognised: S. mannii H. Wendl., which is relatively widespread from Liberia to the Democratic Republic of Congo; S. walkeri A. Chev., which is apparently confined to the interior of Gabon and a band along the Congo River; and S. profiziana, a new species previously considered conspecific to S. mannii that is found in southwest Ghana, Congo, the Democratic Republic of Congo and Angola. The taxonomic history, morphology, distribution and conservation status of the genus and each species are discussed.     

Coffeatoshii sp. nov. (Rubiaceae) from Madagascar

A new species of Coffea from southern central Madagascar, C. toshii, is described and illustrated. The new species is similar to C. buxifolia but differs due to its short, broad spreading habit (vs narrow habit), conspicuous domatia (vs inconspicuous), consistently red fruit (vs reddish purple to dull purple or red), longer fruiting pedicel (vs shorter), presence of bracts (vs absence) and occurrence at lower elevations (vs high elevation).     

Micropera tibetica sp. nov. (Orchidaceae) from southeastern Tibet,China

A new species of Orchidaceae, Micropera tibetica from Medog County, Tibet, China, is described and illustrated. It is morphologically similar to M. mannii, from which it differs by having creamy white flowers, not twisted column, strongly oblique lateral sepals with emarginated apex, and very small lateral lobes of the lip.     

Development and characterization of microsatellite markers for Psychotria tenuinervis (Rubiaceae), a shrub species from the Atlantic forest, and primers transferability from Coffea

The shrub species Psychotria tenuinervis (Rubiaceae) is native to the Brazilian Atlantic forest and is largely found within natural and disturbed forest fragments. Aiming to develop studies on population genetic structure of forest fragment species, eigth microsatellite markers were developed for P. tenuinervis. Also, 15 loci already developed for Coffea (Rubiaceae) were tested for transferability to this species. We utilized 45 individuals from natural populations of three different fragments-anthropic edge, interior fragment and natural edge, within the Brazilian Atlantic forest. The average number of alleles per locus was 2.5 (two–four alleles/locus). These loci will be useful for future population genetic studies aiming to the conservation and management of this species.     

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species

The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea species, C. arabica, C. canephora (Robusta), and C. liberica, native to intertropical Africa have been introduced to New Caledonia. On this archipelago, a secondary contact zone has been characterized where these species coexist, persist, and hybridize spontaneously. We investigated the impact of environmental changes undergone by each species following its introduction in New Caledonia on flowering phenology and overcoming reproductive barriers between sister species. We developed species distribution models and compared both environmental envelopes and climatic niches between native and introduced hybrid zones. Flowering phenology was monitored in a population in the hybrid zone along with temperature and precipitation sequences recorded at a nearby weather station. The extent and nature of hybridization events were characterized using chloroplast and nuclear microsatellite markers. The three Coffea species encountered weak environmental suitability compared to their native ranges when introduced to New Caledonia, especially C. arabica and C. canephora. The niche of the New Caledonia hybrid zone was significantly different from all three species' native niches based on identity tests (I Similarity and D Schoener's Similarity Indexes). This area appeared to exhibit intermediate conditions between the native conditions of the three species for temperature‐related variables and divergent conditions for precipitation‐related ones. Flowering pattern in these Coffea species was shown to have a strong genetic component that determined the time between the triggering rain and anthesis (flower opening), specific to each species. However, a precipitation regime different from those in Africa was directly involved in generating partial flowering overlap between species and thus in allowing hybridization and interspecific gene flow. Interspecific hybrids accounted for 4% of the mature individuals in the sympatric population and occurred between each pair of species with various level of introgression. Adaptation to new environmental conditions following introduction of Coffea species to New Caledonia has resulted in a secondary contact between three related species, which would not have happened in their native ranges, leading to hybridization and gene flow.     

L-丙氨酸对海南粗榧悬浮细胞合成三尖杉酯类碱的影响

该研究在海南粗榧悬浮细胞培养的不同阶段(5、10、15、20 d),分别添加不同剂量的L-丙氨酸(10、30、50、100 mg·L~(-1)),测定细胞生长、细胞活力及产物含量,确定L-丙氨酸最佳的添加时间及添加剂量。结果表明:添加L-丙氨酸对细胞生长和细胞活力均有抑制作用;在海南粗榧悬浮培养第15天、添加30 mg·L~(-1)L-丙氨酸时,产物含量最高(4.853 6 mg·L~(-1)),是对照(2.853 8 mg·L~(-1))的1.7倍。同时,为了探讨添加L-丙氨酸对海南粗榧悬浮细胞糖代谢的影响,对培养基糖耗程度、细胞内糖酵解途径(glycolytic pathway,EMP途径)关键酶丙酮酸激酶(Pyruvate kinase,PK)活力、磷酸戊糖途径(hexose monophosphate pathway,HMP途径)关键酶6-磷酸葡萄糖脱氢酶(glucose 6-phosphate dehydrogenase,G6PDH)活力进行了测定,结果显示添加L-丙氨酸后,植物细胞培养液中总耗糖速度与对照相比无明显差异,丙酮酸激酶(PK)活力与对照(25.37 U·g~(-1))相比下降了29.10%,G6DPH活力是对照组(53.49 U·g~(-1))的1.33倍。以上结果说明,糖代谢途径中碳通量在一定程度上由EMP途径转向了HMP途径,三尖杉酯类碱合成的前体物PEP积累,E4P合成量增加,均有利于产物三尖杉酯类碱含量的增加。     

RAPD and organelle specific PCR re-affirms taxonomic relationships within the genus Coffea

The phenetic relationships between 18 Coffea accessions representing 11 of the most important Coffea species employed in current breeding programmes were examined using RAPD markers and chloroplast and mitochondrial genome specific sequence tagged sites (STS). Estimates of variability based on the number of shared RAPD amplification products placed the species into three distinct groups which were consistent with derived chloroplast DNA phenotypes, the geographical origins of the species and previous studies based on morphological characteristics and RFLPs. C. eugenioides (2n = 2x = 22) exhibited the greatest similarity to the cultivated C. arabica (2n = 4x = 44) and may represent its maternal progenitor. The results are discussed in the context of strategies for Coffea improvement.     

The founding of Mauritian endemic coffee trees by a synchronous long‐distance dispersal event

The stochastic process of long‐distance dispersal is the exclusive means by which plants colonize oceanic islands. Baker's rule posits that self‐incompatible plant lineages are unlikely to successfully colonize oceanic islands because they must achieve a coordinated long‐distance dispersal of sufficiently numerous individuals to establish an outcrossing founder population. Here, we show for the first time that Mauritian Coffea species are self‐incompatible and thus represent an exception to Baker's rule. The genus Coffea (Rubiaceae) is composed of approximately 124 species with a paleotropical distribution. Phylogenetic evidence strongly supports a single colonization of the oceanic island of Mauritius from either Madagascar or Africa. We employ Bayesian divergence time analyses to show that the colonization of Mauritius was not a recent event. We genotype S‐RNase alleles from Mauritian endemic Coffea, and using S‐allele gene genealogies, we show that the Mauritian allelic diversity is confined to just seven deeply divergent Coffea S‐RNase allelic lineages. Based on these data, we developed an individual‐based model and performed a simulation study to estimate the most likely number of founding individuals involved in the colonization of Mauritius. Our simulations show that to explain the observed S‐RNase allelic diversity, the founding population was likely composed of fewer than 31 seeds that were likely synchronously dispersed from an ancestral mainland species.     

Analysis of alien introgression in coffee tree (<Emphasis Type="Italic">Coffea</Emphasis><Emphasis Type="Italic">arabica</Emphasis> L.)

The transfer of desired traits from related wild diploid Coffea species into the cultivated allotetraploid C. arabica is essential in coffee breeding to develop pest/disease-resistant cultivars. The present work is an attempt to gain insights into alien introgression in C. arabica. An F2 population derived from a cross between T5296 and Et6 was analysed with simple sequence repeat (SSR; microsatellite) and amplified fragment length polymorphism (AFLP) molecular markers. The T5296 is a derivative of an interspecific hybrid introgressed by the diploid C. canephora species and Et6 is a wild Ethiopian accession of C. arabica. The origin of the revealed polymorphism was determined by comparisons using representative accessions from C. arabica and its two diploid parental species, C. eugenioides and C. canephora. The number and mode of inheritance of canephora-introgressed segments were investigated, as well as their sub-genome localisation and rate of recombination. The results suggested that the transfer of desirable genes into C. arabica from C. canephora is not limited by the ploidy level differences or the suppression of recombination between the different genomes.     

SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus

Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST–SSRs) with a motif length of 1–6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST–SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST–SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies.     

Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar

Phylogeographic analysis of the Coffea subgenus Coffea was performed using data on plastid DNA sequences and interpreted in relation to biogeographic data on African rain forest flora. Parsimony and Bayesian analyses of trnL-F, trnT-L and atpB-rbcL intergenic spacers from 24 African species revealed two main clades in the Coffea subgenus Coffea whose distribution overlaps in west equatorial Africa. Comparison of trnL-F sequences obtained from GenBank for 45 Coffea species from Cameroon, Madagascar, Grande Comore and the Mascarenes revealed low divergence between African and Madagascan species, suggesting a rapid and radial mode of speciation. A chronological history of the dispersal of the Coffea subgenus Coffea from its centre of origin in Lower Guinea is proposed. No relation was found between phylogenetic topology and the age of emergence of the volcanic islands that Coffea species have colonised in the Indian Ocean, suggesting dispersal from mainland Africa after the emergence of the youngest island, Grande Comore, 500,000 years ago. Additional sequences were obtained from GenBank for 24 species of other Rubiaceae genera, including the Rubia genus whose origin has been dated from the Upper Miocene. Estimates of substitution rates suggested that diversification in Coffea subgenus Coffea occurred about 460,000 years ago or as recently as the last 100,000 years, depending on the cpDNA region considered and calibration. The phylogenetic relationships based on plastid sequences confirmed biogeographic differentiation of coffee species, but they were not congruent with morphological and biochemical classifications, or with the capacity to grow in specific environments. Examples of convergent evolution in the main clades are given using characters of leaf size, caffeine content and reproductive mode.     

Agapetes yingjiangensis (Ericaceae), a new epiphytic species of A. ser. Longifiles from Yunnan,China

Agapetes yingjiangensis (Ericaceae), a new species from Yingjiang County, Yunnan Province, China is described and illustrated. This new species is somewhat similar to A. mannii Hemsl., but differs in having brown‐hirsute young branches, acute mucronate apex of the leaf blade and sparsely hirsute pedicel, calyx tube and corolla. A key to Chinese species with small (less than 2.5 cm) entire leaves in Agapetes sect. Agapetes ser. Longifiles is included.     

Lactones,flavonoids and benzophenones from Garcinia conrauana and Garcinia mannii

Two novel lactones have been isolated from the stem barks of Garcinia conrauana and G. mannii. The major component of the bark of G. conrauana was identified as 3-(3$\text{,}\text{?}$ 3″-dimethylallyl)-conrauanalactone [4-hydroxy-3-(3″, 3″-dimethylallyl)-6-pentadecylpyran- 2-one] by comparison of spectral data of the isolated compound and two methylethers with that obtained for the previously isolated conrauanalactone. A minor component of the bark of G. mannii was tentatively identified as 3-α-hydroxy-5-(heptadec-8′-enyl)-tetrahydro- furan-2-one on the basis of spectral data from the isolated compound and its monoacetate. The distributions of biflavonoids and related compounds and benzophenones in the stem bark, heartwood, seeds and leaves of the two species are reported.