#phylogeneticanalysis

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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.

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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.

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Abstract The pea is an important cool-season pulse crop cultivated for animal and human consumption. However, the presence of “flatulence-causing factors” hinders its consumption and acceptance worldwide. The raffinose family oligosaccharides (RFOs) have been identified as the principal “flatulence causing factors”. Hence, reducing RFO level is the major goal to promote pea consumption and acceptance worldwide. However, very little is known about the genes involved in RFO metabolism at the genome-wide scale in pea. In the present study, genes for five key enzymes (galactinol synthase, raffinose synthase, stachyose synthase, alpha-galactosidase_Acid/Alkaline and beta-fructofuranosidase) involved in RFO metabolism pathway were identified at the genome-wide scale in pea. A total of two galactinol synthase, two raffinose synthase, one stachyose synthase, six alpha-galactosidase_Alkaline and three alpha-galactosidase_Acid and ten beta-fructofuranosidase genes were identified in the pea genome. Phylogenetic relationships analysis, exon/intron structure as well as conserved domain within each enzyme family and their chromosomal location were also determined to establish their relationship with the known proteins. In silico anlaysis showed that pea RFO genes contain 26 microsatellite loci. Taken together, this study provides useful candidate genes for improving the nutritional quality of pea through genetic engineering approaches as well as microsatellite loci for the development of SSR markers for the introgression of low RFO trait through marker assisted selection.

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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.