Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae).

Neomicrocalamus and Temochloa are closely related to bamboo genera. However, when considered with newly discovered and morphologically similar material from China and Vietnam, the phylogenetic relationship among these three groups was ambiguous in the analyses based on DNA regions. Here, as a means of investigating the relationships among the three bamboo groups and exploring potential sources of genomic conflicts, we present a phylogenomic examination based on the whole plastome, single-nucleotide polymorphism (SNP), and single-copy nuclear (SCN) gene datasets. Three different phylogenetic hypotheses were found. The inconsistency is attributed to the combination of incomplete lineage sorting and introgression. The origin of newly discovered bamboos is from introgressive hybridization between Temochloa liliana (which contributed 80.7% of the genome) and Neomicrocalamus prainii (19.3%), indicating that the newly discovered bamboos are closer to T. liliana in genetics. The more similar morphology and closer distribution elevation also imply a closer relationship between Temochloa and newly discovered bamboos.

Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses.

BACKGROUND: Justicia L. is the largest genus in Acanthaceae Juss. and widely distributed in tropical and subtropical regions of the world. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies were mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp.) genomes of 12 Asian plants and combined with the previously published cp. genome of Justicia leptostachya Hemsl. for further comparative genomics and phylogenetic analyses. RESULTS: All the cp. genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434-83,676 bp), a small single copy (SSC, 16,833-17,507 bp) and two inverted repeats (IR, 24,947-25,549 bp). GC contents range from 38.1 to 38.4%. All the plastomes contain 114 genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa C. B. Clarke is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for the genus Justicia. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with the morphology evolution. CONCLUSION: Our study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.

Kengiochloa, a new bamboo genus to accommodate the morphologically unique species, Pseudosasapubiflora (Poaceae).

Pseudosasa was confirmed as polyphyletic by recent phylogenetic analyses, with Chinese species of Pseudosasa distantly related to those from Japan. Among the Chinese species of Pseudosasa, Pseudosasapubiflora is a morphologically unique as well as taxonomically problematic species endemic to South China, of which the generic designation is still uncertain. Molecular analyses based on both plastid and nuclear genomic data demonstrated that this species is closest to the recently published genus Sinosasa. Morphologically, the two are somewhat similar to each other in flowering branches developing at the nodes of every order of branches, raceme-like units of inflorescence with 3-5 short spikelets, each spikelet with few florets including a rudimentary one at the apex, and each floret with 3 stamens and 2 stigmas. However, P.pubiflora is very different from Sinosasa species in many reproductive and vegetative characters, such as the morphology of paracladia (lateral spikelet "pedicels"), the absence or existence of pulvinus at the base of paracladia, the relative length of the upper glume and the lowest lemma, the shape of lodicules and primary culm buds, the branch complement, the morphology of nodes, culm leaves and dried foliage leaf blades, and the number of foliage leaves per ultimate branchlet. The morphological and molecular evidence warrants recognition of a new genus to accommodate this unique species, which is here named Kengiochloa. After consulting related literature and examination of herbarium specimens or specimen photos, a taxonomic revision of K.pubiflora and its synonyms was made, and it was confirmed that four names, viz. P.gracilis, Yushanialanshanensis, Arundinariatenuivagina and P.parilis, should be merged with K.pubiflora, while Indocalamuspallidiflorus and Acidosasapaucifolia are distinct species.

Chimonobambusasangzhiensis (Poaceae, Bambusoideae), a new combination supported by morphological and molecular evidence.

This study elucidates the taxonomic position of Indosasasangzhiensis in considering whether it belongs to Indosasa or Chimonobambusa. Based on morphological and molecular phylogenetic evidence, our results explicitly indicated that I.sangzhiensis should be a member of Chimonobambusa, rather than Indosasa, and is a distinct species closely related to C.communis, C.opienensis and C.puberula. Thus, the new combination Chimonobambusasangzhiensis (B.M.Yang) N.H.Xia & Z.Y.Niu is made. A detailed description as well as two color plates of this species are also provided.

Influence of Soil Organic Carbon on the Aroma of Tobacco Leaves and the Structure of Microbial Communities.

The soil organic carbon is associated with the plant quality and the microbial community structure. In the present study, carbon fertilizers were applied to paddy soil to elucidate the relationship between soil carbon and neutral aroma substances in both tobacco and soil microbiome by transcriptome sequencing and 16S rDNA-based analysis, respectively. Our results showed that (1) the increase in soil carbon content was closely correlated with the abundance of microorganisms belonging to two classes (which could potentially affect tobacco plants), namely Gammaproteobacteria and Chloroflexia, (2) soil carbon apparently affected tobacco neutral aroma substances, and (3) soil carbon improved neutral aroma substances by affecting the transcriptional processes of sesquiterpenoid and chlorophyll biosyntheses. These results suggest that increased soil carbon-especially active organic carbon-resulted in desirable improvements in aroma substances in tobacco leaves.

Transcriptome sequencing reveals the effect of biochar improvement on the development of tobacco plants before and after topping.

The application of biochar is one of the most useful methods for improving soil quality, which is of the utmost significance for the continuous production of crops. As there are no conclusive studies on the specific effects of biochar application on tobacco quality, this study aimed to improve the yield and quality of tobacco as a model crop for economic and genetic research in southern China, by such application. We used transcriptome sequencing to reveal the effects of applied biochar on tobacco development before and after topping. Our results showed that topping affected carbon and nitrogen metabolism, photosynthesis and secondary metabolism in the tobacco plants, while straw biochar-application to the soil resulted in amino acid and lipid synthesis; additionally, it affected secondary metabolism of the tobacco plants through carbon restoration and hormonal action, before and after topping. In addition to the new insights into the impact of biochar on crops, our findings provide a basis for biochar application measures in tobacco and other crops.

Biochar application significantly affects the N pool and microbial community structure in purple and paddy soils.

BACKGROUND: The increasing demand for food production has resulted in the use of large quantities of chemical fertilizers. This has created major environmental problems, such as increased ammonia volatilization, N2O emission, and nitrogen (N) leaching from agricultural soil. In particular, the utilization rate of N fertilizer is low in subtropical southern parts of China due to high rainfall. This causes not only large financial losses in agriculture, but also serious environmental pollution. METHODS: In this study, 16S rDNA-based analysis and static-chamber gas chromatography were used to elucidate the effects of continuous straw biochar application on the N pool and bacteria environment in two typical soil types, purple and paddy soils, in southern China. RESULTS: Straw biochar application (1) improved the soil N pool in both rhizosphere and non-rhizosphere soils; (2) significantly reduced the emission of N2O, with no difference in emission between 1 and 2 years of application; (3) increased the abundance of N-processing bacteria in the soil and altered the bacterial community structure; and (4) improved the tobacco yield and N use efficiency in paddy soil. These findings suggest that, in southern China, the application of straw biochar can promote N transformation in purple and paddy soils and reduce the emission of the greenhouse gas N2O.

Biochar application on paddy and purple soils in southern China: soil carbon and biotic activity.

Soil carbon reserves are the largest terrestrial carbon pools. Common agricultural practices, such as high fertilization rates and intensive crop rotation, have led to global-scale environmental changes, including decreased soil organic matter, lower carbon/nitrogen ratios and disruption of soil carbon pools. These changes have resulted in a decrease in soil microbial activity, severe reduction in soil fertility and transformation of soil nutrients, thereby causing soil nutrient imbalance, which seriously affects crop production. In this study, 16S rDNA-based analysis and static chamber-gas chromatography were used to elucidate the effects of continuous application of straw biochar on soil carbon pools and the soil microbial environments of two typical soil types (purple and paddy soils) in southern China. Application of biochar (1) improved the soil carbon pool and its activity, (2) significantly promoted the release of soil CO2 and (3) improved the soil carbon environment. Soil carbon content was closely correlated with the abundance of organisms belonging to two orders, Lactobacillales and Bacteroidales, and, more specifically, to the genus Lactococcus. These results suggest that biochar affects the soil carbon environment and soil microorganism abundance, which in turn may improve the soil carbon pool.

The complete chloroplast genome of a Chinese endemic ornamental plant Sorbus unguiculata Koehne (Rosaceae).

Sorbus unguiculata is a pinnate-leaved deciduous shrub growing in mixed forests in Sichuan province, China. It is one of the least known species in the genus with high ornamental value. In this study, we firstly assembled and annotated the complete chloroplast genome of the species using the next-generation sequencing method. The results showed that the chloroplast genome size is 159,900 bp, comprising of a large single-copy (LSC) region of 87,888 bp, a small single-copy (SSC) region of 19,256 bp, and a pair of IR regions of 26,378 bp. The whole cp genome predicted 109 genes in total, including 76 protein-coding genes, 29 tRNAs, and 4 tRNAs. The overall GC content of the chloroplast genome is 36.6%. The phylogenetic relationship exhibited that S. unguiculata is closely clustered with S. helenae in Sorbus.