Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba.

Plastid genomes (plastomes) of photosynthetic angiosperms are for the most part highly conserved in their organization, mode of inheritance and rates of nucleotide substitution. A small number of distantly related lineages share a syndrome of features that deviate from this general pattern, including extensive genomic rearrangements, accelerated rates of nucleotide substitution, biparental inheritance and plastome-genome incompatibility. Previous studies of plastomes in Passiflora with limited taxon sampling suggested that the genus exhibits this syndrome. To examine this phenomenon further, 15 new plastomes from Passiflora were sequenced and combined with previously published data to examine the phylogenetic relationships, genome organization and evolutionary rates across all five subgenera and the sister genus Adenia. Phylogenomic analyses using 68 protein-coding genes shared by Passiflora generated a fully resolved and strongly supported tree that is congruent with previous phylogenies based on a few plastid and nuclear loci. This phylogeny was used to examine the distribution of plastome rearrangements across Passiflora. Multiple gene and intron losses and inversions were identified in Passiflora with some occurring in parallel and others that extended across the Passifloraceae. Furthermore, extensive expansions and contractions of the inverted repeat (IR) were uncovered and in some cases this resulted in exclusion of all ribosomal RNA genes from the IR. The most highly rearranged lineage was subgenus Decaloba, which experienced extensive IR expansion that incorporated up to 25 protein-coding genes usually located in large single copy region. Nucleotide substitution rate analyses of 68 protein-coding genes across the genus showed lineage- and locus-specific acceleration. Significant increase in dS, dN and dN/dS was detected for clpP across the genus and for ycf4 in certain lineages. Significant increases in dN and dN/dS for ribosomal subunits and plastid-encoded RNA polymerase genes were detected in the branch leading to the expanded IR-clade in subgenus Decaloba. This subgenus displays the syndrome of unusual features, making it an ideal system to investigate the dynamic evolution of angiosperm plastomes.

The rediscovery of Passiflora kwangtungensis Merr. (subgenus Decaloba supersection Disemma): a critically endangered Chinese endemic.

Passiflora kwangtungensis is a critically endangered Chinese species known from Guangxi, Guangdong, and Jiangxi Provinces. The species belongs to Passiflora subgenus Decaloba, supersection Disemma, section Octandranthus. Field observations decreased rapidly during the 1970s to 1980s, and it was suspected that this species might have been extirpated due to repeated deforestation events throughout southern China. In recent years, however, small isolated populations of this species have been rediscovered in Hunan Province, representing new locality records for Passiflora kwangtungensis. New herbarium collections, color photographs, and silica gel collections have provided an unexpected opportunity to examine the evolutionary significance of this species. The current study presents a revised morphological description of Passiflora kwangtungensis based on fresh material, along with an updated distribution map. Using nrITS sequence data, preliminary insights into the phylogenetic position of Passiflora kwangtungensis are presented. Molecular data support the placement of Passiflora kwangtungensis within supersection Disemma section Octandranthus. However, the exact placement of Passiflora kwangtungensis within this lineage is unclear. The nrITS data suggest that Passiflora kwangtungensis may be sister to a clade containing Passiflora from China, Nepal, India, and Southeast Asia. Morphologically, Passiflora kwangtungensis displays the most similarity Passiflora geminiflora (Nepal, India) and Passiflora henryi (China). Lastly, conservation status and recommendations are made for Passiflora kwangtungensis following the IUCN Red List Criteria, where this species is classified as CR C1+C2a(i); D.

Patterns of anomalous floral development in the Asian Passiflora (subgenus Decaloba: supersection Disemma).

Approximately 22 species of Passiflora are native to the Old World. All of these species are placed in subgenus Decaloba, supersection Disemma. Within Disemma, three species vary in stamen and carpel number (≤ eight stamens and five carpels). The mode of development was determined for two of the anomalous species, P. moluccana var. glaberrima and P. siamica. Ontogenetic patterns were compared to normal development in P. perakensis and P. holosericea. Passiflora siamica develops additional stamens through dédoublement of a single widened stamen primordium, while P. moluccana var. glaberrima exhibits congenital dédoublement where stamens emerge already doubled. Phylogenetic analysis using ITS and the trnL-F intron and spacer resolve the anomalous species as monophyletic and sister to P. perakensis. This signifies a single loss of genetic regulation in stamen and carpel number within Disemma. Floral whorls were examined across the Passifloraceae, Malesherbiaceae, Turneraceae, and Flacourtiaceae s.l.. Similar doubling in these families suggests that this Eurosid lineage may have a genetic propensity for variability in floral whorl number.