#phylogeneticanalysis

Abstract Apples are one of the most popular and economically important fruits worldwide and have both nutritional and ornamental value. However, because of their complexity, studies on apple mitochondrial (mt) genomes have been limited. In this study, the mt genomes of Aksu Fuji and Ralls Janet cultivars were assembled, annotated, and analyzed based on a hybrid strategy using Illumina, and comprehensive comparisons of their structure, gene content, intercellular gene transfer, phylogeny, and RNA editing sites were performed. The mt genome length and gene structure of the two apple cultivars were identical (396 592 bp) and included 63 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. There were 44 and 31 mitochondrial plastid fragments (MTPTs) identified between the mt and plastid genomes of the Ralls Janet and Aksu Fuji cultivars, accounting for 1.98 and 2.19% of their mt genomes, respectively. Furthermore, there were 419 and 421 RNA editing sites were detected in Aksu Fuji and Ralls Janet, respectively. Analyses of coding usage bias, nucleotide diversity, selection pressure, and genetic distance revealed that the mt genomes of the two cultivars were highly conserved. Phylogenetic analysis of 29 Rosaceae species showed that Aksu Fuji and Ralls Janet clustered with Malus baccata and M. kansuensis. This study provides new insights into the genetics, systematics, and evolution of apple mt genomes.

Abstract Leafhoppers, a broad group of Hemiptera insects, are economic pests that wreak havoc on agriculture and forestry. The genus Ossuaria was established by Dworakowska in 1979, Zhang and Yang discovered Ossuaria sichuanensis (Zhang and Yang, 2011) from China in 2011, but there is no molecular biological evidence to record the genus. To report complete mitochondrial genome of O. sichuanensis, DNA was extracted from the muscle tissue of adult insect and sequenced. The original data were assembled and annotated, a complete mitochondrial genome was mapped, and phylogenetic analysis was performed using maximum likelihood and Bayesian inference. The circular mitogenome of O. sichuanensis is 15.558 bp in length and including 37 typical genes (13 PCGs, 22 tRNA genes, and 2 rRNA genes) and a putative control region. The overall base composition is 42.89% A, 36.92% T, 11.02% C, and 9.17% G, and the A + T content is 79.81%. Phylogenetic analyses confirmed the O. sichuanensis is the sisters of other members of the tribe Erythroneurini. The mitochondrial genome structure agrees with earlier research. The genus Ossuaria has been characterized at the molecular level for the first time, and additional research is required to determine how the tribe Zyginellini and the tribe Typhlocybini are related.

Abstract Background: Worldwide, Pigeonpea (Cajanus cajan L.) is a protein source. SBP-box transcription factors are crucial for plant development and regulation of stress resistance. The SBP genes in Pigeonpea were examined utilizing genomic information. Methods: Using databases, PlantTFDB and NCBI, SBP-box family genes of Pigeonpea were identified and then characterized in silico using bioinformatics tools. Results: In this study, 5 major chromosomes out of 11 and an unplaced scaffold of the Pigeonpea were found to have 24 SBP genes. Significant differences in CcaSBPs protein length, molecular weight, GRAVY value (grand average of hydropathicity), and theoretical isoelectric point were observed. It was shown by Gene Structure Display Server (GSDS) that all CcaSBP genes contain one or more introns. CcaSBP proteins and SBP proteins from other species (A. thaliana and O. sativa) were analyzed phylogenetically and grouped into seven major groups (I–VII). Through this, an effort has been made to present unique information on CcaSBP genes to study Pigeonpea growth and stress mechanisms.

Abstract Clematis tomentella 2001 (Ranunculaceae) is a typical drought-tolerant sand-fixing plant in desert ecosystem in northwest China. To elucidate the phylogenetic status of C. tomentella and its related species, we determined the complete chloroplast (cp) genome and analyzed their interspecific relationships. The result showed that the cp genome of C. tomentella was 159 816 bp in length, including two inverted repeats of 31 045 bp, a large single copy region of 79 535 bp, and a small single copy region of 18 191 bp. 136 genes were annotated across the whole cp genome, including 92 protein-coding genes, 8 rRNA genes, and 36 tRNA genes, as well as the GC content accounted for 38%. Crucially, we found that the regions of psbE-petL, trnG_UCC-atpA, ndhF-rpl32, and rps8-infA were highly divergent, which could be marked as DNA barcodes for the identification of C. tomentella in Ranunculaceae. A maximum likelihood phylogenetic tree revealed that C. tomentella was closely related to C. fruticosa. Our results provide the references and implications for the phylogenetic study of Clematis in Ranunculaceae in the future.

Abstract Stellaria dichotoma L. var. lanceolata Bunge is a typical rare medicinal plant commonly used in therapeutic formulations. To reveal the structural arrangements and variation of complete chloroplast genomes between S. dichotoma var. lanceolata and its related species is of great significance for the study of its evolutionary status. In this study, evolutionary relationships between S. dichotoma var. lanceolata and its related species of Caryophyllaceae were documented based on the complete chloroplast genome sequence of S. dichotoma var. lanceolata. The result showed that the whole circular genome of S. dichotoma var. lanceolata was 150 461 bp in length, annotated 129 genes, possessing RSCU of 21 types of amino acids and 64 codons encoding. By comparing and analyzing the SSR and variation region of the chloroplast gene of S. dichotoma var. lanceolata and its related genus pseudostellaria, the authors found that the divergent regions of trnk-rps16, atpH-atpI, rpoC1-rpoB, rbcL-accD, trnS-trnG, psaA-ycf3, trnV-trnM, ycf4-cemA, petL-petG, trnL-ccsA, ndhF, ndhA, and ycf1 fragments were highly obvious, which could be used as DNA barcodes for the taxonomic evidence of S. dichotoma var. Lanceolata and Pseudostellaria in Caryophyllaceae. A maximum likelihood (ML) phylogenetic tree elucidated that S. dichotoma var. lanceolata was closely related to pseudostellaria and cluster into a branch with Cerastium. The results lay a robust foundation for future phylogenetic and evolutionary status of S. dichotoma var. lanceolata and among relatives within Caryophyllaceae.