Zhi-Zhong Li

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.

RNA-Seq Analysis of the Distylous Plant Nymphoides peltata Identified Ortholog Genes between Long- and Short-Styled Flowers

Distyly is a floral polymorphism whereby plants in a population display two floral morphs (referred to as the longand short-styled morphs) that differ reciprocally in style length, anther height, and pollen size, etc., which together with a self-incompatibility (SI) system (Barrett et al., 2000; Barrett, 2002). The development of the two different morphs of flower is controlled by a single diallelic locus designated the “S locus” that is a multigene complex (Barrett, 1992). Although, progresses have been made to isolate and characterize the S locus in a number of distylous plant species (Barrett and Shore, 2008; Li et al., 2011; Nowak et al., 2015), the number of S locus genes and the molecular mechanism by which it operates still remain to be uncovered. Heterostylous plants, including distylous or tristylous plants, have been used as a model for genetics and evolutionary biology (Barrett, 1992). Heterostyly is one of the most effective mechanisms to avoid selfing and promote outcrossing in flowering plant (Barrett et al., 2000; Nowak et al., 2015). Heterostyly represent remarkable example of convergent evolution via natural selection and have been found in a wide range of species belonged to at least 28 families (Barrett and Shore, 2008). However, little is known of the nature of evolutionary changes in genes determined by natural selection during the origin and evolution of the heterostyly in flowering plants. Nymphoides peltata (Gmel.) O. Kuntze (Menyanthaceae) is a floating-leaf perennial aquatic plant. This species is a typical distylous plant with dimorphic herkogamy and intramorphand self-incompatibility (Wang, 2005). N. peltata can produce a number of relatively large flowers, and these yellow and showy flowers are produced over a long period of time. This developmental pattern makes it easy to get rich flower organ materials and manipulate in subsequent experiments. Based on above-mentioned features, this species is very suitable for studying the molecular mechanism of heterostyly and has a potential to be a new study system. In this study, we sequenced two floral transcriptomes from longand short-styled flowered plants of this distylous species using the RNA-Seq technique. We also idenfied the divergent orthologous genes between longand short-styled flowers. Our aims were to provide genetic resources for screening genes involved in the development of distyly and for revealing the role of natural selection in driving the floral morph diversity in the evolution of distylous plant.

Lobelia hongiana (Campanulaceae), a new species from Guangxi, China

Abstract Lobelia hongiana, a new species of Campanulaceae from Guangxi, South China, is described and illustrated here. This new species is most similar to L. chinensis and L. loochooensis, but differs by its elliptic-obovate or oblanceolate leaf, 2.5–3 mm long greenish-carmine hypanthium, 5 or 6 calyx lobes, purplish-white corolla, with yellowish-green blotches at the base of lower lobes, glabrous filaments, 7–8 mm long broadly obconic capsule. Molecular phylogenetic analysis has been conducted based on ITS and two chloroplast sequences (atpB and rbcL) and 14 taxa in Lobelia are included. L. hongiana is well supported as a new species by the evidence from both morphology and molecular phylogeny.

Genetic diversity and population structure of the endangered basal angiosperm Brasenia schreberi (Cabombaceae) in China

Brasenia schreberi J.F. Gmelin (Cabombaceae), an aquatic herb that occurs in fragmented locations in China, is rare and endangered. Understanding its genetic diversity and structure is crucial for its conservation and management. In this study, 12 microsatellite markers were used to estimate the genetic diversity and variation in 21 populations of B. schreberi in China. A total of 61 alleles were found; assessment of allelic richness (Ar = 1.92) and observed and expected heterozygosity (HO = 0.200, HE = 0.256) suggest lower genetic diversity compared to some endangered species, and higher variation was observed within populations (58.68%) rather than among populations (41.32%). No significant correlation between geographical and genetic distance among populations was detected (Mantel test, r = 0.0694; P = 0.7985), which may have likely resulted from barriers to gene flow (Nm = 0.361) that were produced by habitat fragmentation. However, Bayesian and neighbor-joining cluster analyses suggest a population genetic structure consisting of two clusters (I and II) or four subclusters (I-1, 2 and II-1, 2). The genetic structure and distribution of B. schreberi in China may have involved glacial refugia that underwent range expansions, introgression, and habitat fragmentation. The findings of the present study emphasize the importance for both in situ and ex situ conservation efforts.

Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae)

Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum.

Development and Characterization of EST-SSR Markers for Ottelia acuminata var. jingxiensis (Hydrocharitaceae)

Premise of the study: Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Methods and Results: Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis. One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata, and 12 amplified in each of the other three varieties of O. acuminata. Conclusions: These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata.