Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis).

BACKGROUND: Leaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll (Chl) biosynthesis and metabolism regulation. RESULTS: In this study, we identified a stably inherited yellow leaf mutant derived from 'Huaguan' pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1520 F3:4 yellow-colored individuals co-segregated with py1. For py2, 1860 recessive homozygous F3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm. CONCLUSIONS: Our study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation.

Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina.

BACKGROUND: Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny. Comprehensive analysis of the CUB of mitochondrial (mt) genes can provide rich genetic information for improving the expression efficiency of exogenous genes and optimizing molecular-assisted breeding programmes in H. citrina. RESULTS: Here, the CUB patterns in the mt genome of H. citrina were systematically analyzed, and the possible factors shaping CUB were further evaluated. Composition analysis of codons revealed that the overall GC (GCall) and GC at the third codon position (GC3) contents of mt genes were lower than 50%, presenting a preference for A/T-rich nucleotides and A/T-ending codons in H. citrina. The high values of the effective number of codons (ENC) are indicative of fairly weak CUB. Significant correlations of ENC with the GC3 and codon counts were observed, suggesting that not only compositional constraints but also gene length contributed greatly to CUB. Combined ENC-plot, neutrality plot, and Parity rule 2 (PR2)-plot analyses augmented the inference that the CUB patterns of the H. citrina mitogenome can be attributed to multiple factors. Natural selection, mutation pressure, and other factors might play a major role in shaping the CUB of mt genes, although natural selection is the decisive factor. Moreover, we identified a total of 29 high-frequency codons and 22 optimal codons, which exhibited a consistent preference for ending in A/T. Subsequent relative synonymous codon usage (RSCU)-based cluster and mt protein coding gene (PCG)-based phylogenetic analyses suggested that H. citrina is close to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in evolutionary terms, reflecting a certain correlation between CUB and evolutionary relationships. CONCLUSIONS: There is weak CUB in the H. citrina mitogenome that is subject to the combined effects of multiple factors, especially natural selection. H. citrina was found to be closely related to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in terms of their evolutionary relationships as well as the CUB patterns of their mitogenomes. Our findings provide a fundamental reference for further studies on genetic modification and phylogenetic evolution in H. citrina.

Hydrothermal regulation of MnO2 on a wood-based RGO composite for achieving wide voltage windows and high energy density supercapacitors.

The increasing need for improved energy storage devices renders it particularly important that inexpensive electrodes with high capacitance, excellent cycling stability, and environment-friendly characteristics are developed. In this study, a wood-derived carbon@reduced graphene (WRG) conductive precursor with an average conductivity of 15.38 S/m was firstly synthesized. The binder-free WRG-MnO2 electrode was successfully constructed by growing MnO2 onto a WRG under hydrothermal conditions. The asymmetric supercapacitor assembled with the WRG-20MnO2 cathode exhibited excellent electrochemical capacitive behavior with a voltage window of 0-2 V, maximum energy density of 52.3 Wh kg-1, and maximum power density of 1642.7 W kg-1, which is mainly due to the distinctive icicle-shaped structure of the MnO2. Thus, a facile strategy for developing high-performance hierarchical porous carbon electrodes that can be used in supercapacitors was developed herein, which may provide new opportunities to improve the high added value of poplar wood.

Deciphering the mitochondrial genome of Hemerocallis citrina (Asphodelaceae) using a combined assembly and comparative genomic strategy.

Hemerocallis citrina is a perennial herbaceous plant that is dedicated to mothers in Chinese culture and is widely distributed across the country. As a popular species with a long history of cultivation and utilization, it is renowned for its remarkable edible and medicinal value. In this study, we integrated Illumina short-read and Oxford Nanopore long-read sequencing to generate a complete mitochondrial genome (mitogenome) assembly of H. citrina. The H. citrina mitogenome has a multiple chromosomal structure consisting of three circular molecules that are 45,607 bp, 239,991 bp, and 182,864 bp long. We correspondingly annotated 66 genes, comprising 45 protein-coding genes (PCGs), 17 tRNA genes, and 4 rRNA genes. Comparative analysis of gene organization indicated that six syntenic gene clusters were conserved in the mitogenomes of the compared plants. The investigation of repeat content revealed repeat-rich nature of the H. citrina mitogenome, for which plentiful dispersed repeats were characterized to correlate with the size of the mitogenome. The codon usage behavior disclosed that Leucine (Leu) and Serine (Ser) were the most preferred amino acids in H. citrina, and nearly all of the codons with relative synonymous codon usage (RSCU) values greater than 1 showed the preference of A or T ending. Moreover, we inferred a total of 679 RNA editing sites in all mitochondrial PCGs, which presented perfect C-to-U types and tended to lead to the alteration of internal codons. Subsequent selective pressure analysis showed that the majority of the PCGs had undergone evolutionary negative selections, with atp9 in particular undergoing strong stabilizing selection, reflecting its indispensable function in mitogenomes. According to the phylogenetic analysis, H. citrina is close to the species Allium cepa (Amaryllidaceae) and Asparagus officinalis (Asparagaceae) in evolutionary terms. Overall, this project presents the first complete mitogenome of H. citrina, which could provide a reference genome for the comprehensive exploration of the Asphodelaceae family and can facilitate further genomic breeding and evolutionary research on this medicine-food homologous plant.

The complete chloroplast genome sequence of the medicinal plant Persicaria filiformis.

Persicaria filiformis, known as a traditional Chinese herbal medicine, is a perennial plant of Polygonaceae wildly distributed in China. The complete chloroplast (cp) genome of P. filiformis was assembled and analyzed in this study. The length of the circular genome is 159,741 bp, with a rich GC content of 41.3%. The cp genome structure consists of a large single-copy region (LSC 84,432 bp), a small single-copy region (SSC 13,073 bp) and a pair of inverted repeat regions (IR 31,118 bp). The complete genome encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis indicated that P. filiformis is most related to P. japonica.

The complete chloroplast genome of Choerospondias axillaris (Roxb.) B. L. Burtt et A. W. Hill, an ancient and versatile plant.

Choerospondias axillaris, an ancient and versatile plant of Anacardiaceae, which is widespread in eastern Asia. The complete chloroplast (cp) genome of C. axillaris was generated and determined in this work. The genome of cp was 159,131 bp in length with a total GC content of 37.6%. The circular molecular genome presented a quadripartite structure, comprising a 91,305 bp large single-copy region (LSC), a 19,092 bp small single-copy region (SSC), and a pair of inverted repeat regions with 24,367 bp. The complete genome encoded 128 genes, including 83 protein coding, 37 tRNA and eight rRNA genes. Phylogenetic analysis indicated that C. axillaris was most related to Sclerocarya birrea.

Characterization of the complete chloroplast genome of Tabernaemontana divaricate (Apocynaceae), a valuable and endangered plant.

Tabernaemontana divaricate is a vulnerable species of Apocynaceae with significant medicinal values. In this study, the complete chloroplast (cp) genome of T. divaricate was determined through the Illumina NovaSeq platform. The circular molecular genome was157,954 bp in length with two inverted repeats (IRa and IRb) regions of 25,769 bp, a large single-copy (LSC) region of 88,246 bp, and a small single-copy (SSC) region of 18,170 bp. It contained 131 genes, including 86 protein-coding, 37 tRNA, and eight rRNA genes. Phylogenetic analysis showed that T. divaricata exhibited the closest relationship with Catharanthus roseus and Rauvolfia serpentina.