Low-Copy Nuclear Genes Reveal New Evidence of Incongruence in Relationships Within Malvaceae s. l.

Abstract— The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s. l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plants Project (1KP) and publicly available genome information from cotton, cacao, and Arabidopsis, we designed a set of molecular markers of potentially single- or low-copy nuclear genes for Malvaceae s. l. Phylogenetic potential of these new loci was compared to previously applied conventional markers (i.e. plastid trnK-matK region and rbcL gene and the nrDNA ITS region) using the phylogenetic informativeness method. The results show that, when the mined nuclear regions are used in combination, it is possible to resolve relationships at different taxonomic levels within the phylogeny. However, incongruence among nuclear loci is frequent in the group, explaining the prevalence of unresolved phylogenetic relationships.

A customised target capture sequencing tool for molecular identification of Aloe vera and relatives

Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.

Saccharomyces cerevisiae as a Tool for Studying Mutations in Nuclear Genes Involved in Diseases Caused by Mitochondrial DNA Instability

Mitochondrial DNA (mtDNA) maintenance is critical for oxidative phosphorylation (OXPHOS) since some subunits of the respiratory chain complexes are mitochondrially encoded. Pathological mutations in nuclear genes involved in the mtDNA metabolism may result in a quantitative decrease in mtDNA levels, referred to as mtDNA depletion, or in qualitative defects in mtDNA, especially in multiple deletions. Since, in the last decade, most of the novel mutations have been identified through whole-exome sequencing, it is crucial to confirm the pathogenicity by functional analysis in the appropriate model systems. Among these, the yeast Saccharomyces cerevisiae has proved to be a good model for studying mutations associated with mtDNA instability. This review focuses on the use of yeast for evaluating the pathogenicity of mutations in six genes, MPV17/SYM1, MRM2/MRM2, OPA1/MGM1, POLG/MIP1, RRM2B/RNR2, and SLC25A4/AAC2, all associated with mtDNA depletion or multiple deletions. We highlight the techniques used to construct a specific model and to measure the mtDNA instability as well as the main results obtained. We then report the contribution that yeast has given in understanding the pathogenic mechanisms of the mutant variants, in finding the genetic suppressors of the mitochondrial defects and in the discovery of molecules able to improve the mtDNA stability.

BBX16 mediates the repression of seedling photomorphogenesis downstream of the GUN1-GLK1 module during retrograde signaling

Plastid-to-nucleus retrograde signals (RS) initiated by dysfunctional chloroplasts impact photomorphogenic development. We previously showed that the transcription factor GLK1 acts downstream of the RS-regulator GUN1 in photodamaging conditions to regulate not only the well-established expression of photosynthesis-associated nuclear genes (PhANGs) but also to regulate seedling morphogenesis. Specifically, the GUN1/GLK1 module inhibits the light-induced PIF-repressed transcriptional network to suppress cotyledon development when chloroplast integrity is compromised, modulating the area exposed to potentially damaging high light. However, how the GUN1/GLK1 module inhibits photomorphogenesis upon chloroplast damage remained undefined. Here, we report the identification of BBX16 as a novel direct target of GLK1. BBX16 is induced and promotes photomorphogenesis in moderate light and it is repressed via GUN1/GLK1 after chloroplast damage. Additionally, we show that BBX16 represents a regulatory branching point downstream of GUN1/GLK1 in the regulation of PhANG expression and seedling development upon RS activation. The gun1 phenotype in lincomycin and the gun1-like phenotype of GLK1OX are markedly suppressed in gun1bbx16 and GLK1OXbbx16. This study identifies BBX16 as the first member of the BBX family involved in RS, and defines a molecular bifurcation mechanism operated by GLK1/BBX16 to optimize seedling deetiolation, and to ensure photoprotection in unfavorable light conditions.

Phylogeny of Pyrus and their relationships inferred from sequences of nuclear NIA-i3 intron and chloroplast ndhC-trnV and trnR-atpA

Background: Pear (Pyrus L.) belongs to subtribe Malinae, tribe Maleae, family Rosaceae. According to the geography distribution, it could be divided into Oriental pear and Occidental pear. Though the phylogeny of Pyrus was complicate, previous study referring to morphology, nuclear genes and chloroplast genes made the relationships clear gradually. However, they had lower sequence divergence and less information, therefore it hardly solved the phylogeny of Pyrus. Results: A total of 100 accessions from Oriental and Occidental pears were used to elucidate the phylogeny of Pyrus by one nuclear NIA-i3 intron and two chloroplast regions (ndhC-trnV and trnR-atpA) with higher polymorphism. The Neighbor-Net phylogenetic network indicated that the phylogenetic relationships were complicate based on ndhC-trnV and trnR-atpA. Oriental pear and Occidental pear were separated in the tree of NIA-i3, P. betulaforlia, P. pashia (except P. pashia ‘P10-3’_1 and P. pashia ‘P23-4’_1) were monophyly; several P. ussuriensis were closely related with P. xerophila. However, the phylogenetic relationships of Chinese White Pear, P. pyrifolia and some P. ussuriensis still could not be well solved; West Asian species and European species were mingled together. Occidental pear P. caucasica 684，P. pyraster 989，P. elaeagrifolia 2817 might be hybrids between Oriental pear and Occidental pear.Conclusions: The phylogenetic relationships of Pyrus were still complicate because interspecies and intraspecies of Oriental pear and Occidental pear respectively were intercrossed. More genes and more accessions were needed to solve the phylogenetic relationships in Pyrus and to explore the possible parents.

Targeting PINK1 Using Natural Products for the Treatment of Human Diseases

PINK1, also known as PARK6, is a PTEN-induced putative kinase 1 that is encoded by nuclear genes. PINK1 is ubiquitously expressed and regulates mitochondrial function and mitophagy in a range of cell types. The dysregulation of PINK1 is associated with the pathogenesis and development of mitochondrial-associated disorders. Many natural products could regulate PINK1 to relieve PINK1-associated diseases. Here, we review the structure and function of PINK1, its relationship to human diseases, and the regulation of natural products to PINK1. We further highlight that the discovery of natural PINK1 regulators represents an attractive strategy for the treatment of PINK1-related diseases, including liver and heart diseases, cancer, and Parkinson’s disease. Moreover, investigating PINK1 regulation of natural products can enhance the in-depth comprehension of the mechanism of action of natural products.

Morphological description of a new specimen of Herpetoreas burbrinki Guo et al 2014 (Serpentes: Colubridae)

The original description of Burbrink’s Keelback, Herpetoreas burbrinki was based on a sole damaged specimen collected from Zayu County, Xizang Autonomous Region, China in September 2007. On 16 August 2019, we collected a second live adult female specimen from the type locality. The identity of the species is established based on morphological and molecular comparison with the holotype. One mitochondrial gene (Cytb) and three nuclear genes (C-mos, Rag1, NT3) of the new specimen were sequenced. The four sequences all share the same haplotypes with the holotype. We describe the coloration in life, variation with the type and expand the morphological description of this species.