A new species and a replacement name in Cynanchum (Apocynaceae, Asclepiadeae) from China.

Cynanchumpingtaoi S.Jin Zeng, G.D.Tang & Miao Liao, sp. nov. (Apocynaceae) from Yunnan Province, China, is described and illustrated based on morphological and molecular evidence. Its deeply cordate to reniform leaves and campanulate, large flowers show that it is a member of former Raphistemma Wall., which has been included in Cynanchum L.. It is different from all former Raphistemma species by the broadly ovate corolla lobes, purple-red corolla and connivent corona tip slightly exceeding the corolla throat. Meanwhile, Cynanchumlonghushanense G.D.Tang & Miao Liao, nom. nov. is proposed as replacement name for Raphistemmabrevipedunculatum Y.Wan, which was considered a synonym of Cynanchumhooperianum (Blume) Liede & Khanum but is here reinstated as a distinct species because of significant morphological differences.

Spatial distribution pattern and correlation of dominant populations in the shrub layer of Fengshui forest in Leizhou Peninsula, China.

To elucidate the spatial patterns of understory species in fragmented forests adjacent to human settlements, we examined the spatial distribution and intraspecific correlations of three dominant species Mallotus philippensis, Dasymashalon trichophorum, and Psychotria rubra by employing point pattern analysis, which were the top three in terms of importance value in the shrub layer of Fengshui forest in Leizhou Peninsula, Guangdong. The results showed that all the three species were mainly aggregated at the scale of 0-25 m, especially for young trees. The degree of aggregation gradually diminished with increasing age class. The spatial distribution patterns of three species were predominantly influenced by habitat heterogeneity, negative density dependence, and dispersal limitation. They showed positive association among different age classes, especially between young trees and middle age trees and between young trees and adult trees. Therefore, in the ecological restoration process of Leizhou Peninsula, M. philippensis, D. trichophorum, and P. rubra should be planted in clusters at a small scale within the range of 0-25 m, with the degree of clusters depending on plant morphology. For larger scales, a dispersed cultivation approach was advocated.

Lysimachiadanxiashanensis, a new species of Primulaceae from Guangdong, China.

Lysimachiadanxiashanensis, a new Primulaceae species, endemic to the Danxia landscape in Guangdong Province, China, is described and illustrated. This new species is morphologically similar to L.pseudohenryi, L.phyllocephala, L.congestiflora and L.kwangtungensis, but it differs from the similar species by its purplish-red plants, petiole without wings, calyx with orange glandular and the corolla margin serrated on upper half with orange-red glandular punctates. This new species belongs to Lysimachiasubgen.Lysimachiasect.Nummularia. Phylogenetic analysis confirmed that L.danxiashanensis is a distinct clade, based on the combined data of ITS and rbcL sequences. The conservation status of the new species was evaluated as Endangered (EN) according to IUCN Red List Categories and Criteria.

Diploid and tetraploid genomes of Acorus and the evolution of monocots.

Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.

Complete plastome sequence of Hoya carnosa (L. f.) R. Br. (Apocynaceae).

Hoya is a remarkable genus with high horticultural ornamental value. In this study, we report and characterize the complete plastid genome sequence of Hoya carnosa. The complete chloroplast genome was 176,340 bp in length, which includes a pair of inverted repeat regions (IRs) of 41,381 bp separated by a large single copy region (LSC) 91,281 bp and a small single copy region (SSC) 2,297 bp. Interestingly, IRs expanded into SSC, with the result that most of the genes in SSC were duplicated. This chloroplast genome contained 110 genes, including 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The complete plastome sequence of H. carnosa will provide some useful information for future phylogenetic study of Hoya and its horticultural application.

Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data.

The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau ( τ) using the formula t= τ/2 u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.

The complete chloroplast genome of the highly poisonous plant Cerbera manghas L. (Apocynaceae).

The complete chloroplast genome of Cerber amanghas L., a species of the tribe Plumerieae of the family Apocynaceae, is determined for the first time here. The chloroplast genome is 154,428 bp long, containing a large single-copy region (LSC) of 85,138 bp and a small single-copy region (SSC) of 17,390 bp, which are separated by a pair of 25,950 bp long inverted repeat regions (IRs). It encodes a total of 115 genes, including 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes.Phylogenetic analysis revealed that C.manghas is a member of the paraphyletic tribe Plumerieae of Apocynaceae and is closely related to Thevetia peruviana.

Oreocharis tetrapterus (Gesneriaceae), a new species from East Guangxi, China.

A new species, Oreocharis tetrapterus F.Wen, B.Pan & T.V.Do (Gesneriaceae) from Gupo Mountain area, Hezhou city, Guangxi Zhuangzu Autonomous Region, China, is described and illustrated. The new species has a zygomorphic tetramerous corolla with two adaxial and two abaxial lobes and two fertile stamens in the posterior position, making this a unique combination of floral characteristics in the expanded Oreocharis.

Adding perches for cross-pollination ensures the reproduction of a self-incompatible orchid.

BACKGROUND: Outcrossing is known to carry genetic advantages in comparison with inbreeding. In many cases, flowering plants develop a self-incompatibility mechanism, along with a floral component adaptation mechanism, to avoid self-pollination and to promote outbreeding. Orchids commonly have a lip in their flower that functions as the a visiting plate for insect pollinators. Aside from the lip, however, many species (including Coelogyne rigida) have sheaths around the axis of inflorescence. The function of these sheaths remains unknown, and has long been a puzzle to researchers. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the function of these sheaths in relation to the lip and the pollinators, as well as their role in the modes of pollination and reproduction of Coelogyne rigida in 30 flowering populations of orchids in the limestone area of Southeast Yunnan, China. We found that self-incompatible C. rigida developed specialized bird perches around the basal axis of inflorescence to attract sunbirds and to complement their behavioral tendency to change foraging locations frequently. This self-incompatibility mechanism operates separately from the floral component adaptation mechanism. This mechanism thus prevents bees from repeatedly visiting the floral lip of the same plant which, in turn, results in autogamy. In this way, instead of preventing autogamy, C. rigida responds to these negative effects through a highly efficient cross-pollination method that successfully transfers pollen to different plants. CONCLUSIONS: The proposed method ensures reproductive success, while offsetting the infertile self-pollination by insects, thereby reducing mating costs and addressing the lack of cross-pollination. The adaptation provides a novel and striking example of structural adaptation that promotes cross-pollination in angiosperms.

Pollination: self-fertilization strategy in an orchid.

Mating in flowering plants normally relies on animals, wind, gravity or secretion to convey pollen grains from the male (anther) to the female (stigma) organ. Here we describe a new type of self-pollination mechanism in the tree-living orchid Holcoglossum amesianum, in which the bisexual flower turns its anther against gravity through 360 degrees in order to insert pollen into its own stigma cavity - without the aid of any pollinating agent or medium. This mode of self-pollination, which occurs under windless, drought conditions when insects are scarce, adds to the variety of mechanisms that have evolved in angiosperms to ensure their reproductive success.