Wentao Sheng^1,2,*

Phyton-International Journal of Experimental Botany, Vol.94, No.7, pp. 2015-2031, 2025, DOI:10.32604/phyton.2025.066232 - 31 July 2025

Abstract Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance. This plant has become an important wild relative species for rapeseed (Brassica napus L.) and is used to improve its agronomic traits, with important development and utilization value. However, the research of R. indica genetics is still lacking. And no mitochondrial genome (mitogenome) in the genus Rorippa has been expounded. To analyze the structural characteristics of the R. indica mitogenome, second-generation and third-generation sequencing techniques were made to assemble its mitogenome. The results showed that its mitogenome is composed of a single master… More >

Zichen Li^1,#, Jukui Ma^2,#, Minjun Liu³, Guowei Geng^1,*, Hongxia Zhang^1,*

Phyton-International Journal of Experimental Botany, Vol.94, No.6, pp. 1841-1856, 2025, DOI:10.32604/phyton.2025.066148 - 27 June 2025

Abstract Sweet potatoes are significant cash crops, however, their yield and quality are greatly compromised by viral diseases. In this study, the complete genomic sequences of two Sweet Potato Virus 2 (SPV2) isolates from infected sweet potato leaves in the Shandong (designated as SPV2-SDYT, GenBank No. PQ855660.1) and Jiangsu (designated as SPV2-JSXZ, GenBank No. PQ855661.1) provinces in China were obtained using 5^′ RACE and RT-PCR amplification. Consistency, phylogeny, codon usage bias, recombination, and selection pressure analyses were conducted using the SPV2-SDYT and SPV2-JSXZ genome sequences. The complete genome sequences of SPV2-SDYT and SPV2-JSXZ were 10561 nucleotides (nt)… More >

Xinxin Liu^1,#, Yueyue Zhang^1,#, Rahat Sharif¹, Weiqin Mo², Zhenrong Li¹, Guiling Yang¹, Chao Song¹, Ting Ye^2,*, Changming Chen^1,*

Phyton-International Journal of Experimental Botany, Vol.94, No.6, pp. 1695-1709, 2025, DOI:10.32604/phyton.2025.063349 - 27 June 2025

Abstract The color difference of capsicum fruit is closely related to the type and content of pigment in the peel, which is mainly determined by anthocyanins, chlorophyll, and carotenoids. This study used green “CA59” and purple “Z81” pepper fruits as parents to create the F₂ generation. The fruit color of 466 F₂ population was identified, and the extreme individuals from this population were selected for Bulked Segregant Analysis (BSA) using resequencing. Genetic analysis revealed that a pair of genes controls the expression of the purple fruit trait in capsicum. Using functional annotation, expression analysis, and sequencing analysis… More >

Wentao Sheng^*

Phyton-International Journal of Experimental Botany, Vol.94, No.2, pp. 331-345, 2025, DOI:10.32604/phyton.2025.061424 - 06 March 2025

Abstract Pyrola atropurpurea Franch is an important annual herbaceous plant. Few genomic analyses have been conducted on this plant, and chloroplast genome research will enrich its genomics basis. This study is based on high-throughput sequencing technology and Bioinformatics methods to obtain the sequence, structure, and other characteristics of the P. atropurpurea chloroplast genome. The result showed that the chloroplast genome of P. atropurpurea has a double-stranded circular structure with a total length of 172,535 bp and a typical four-segment structure. The genome has annotated a total of 132 functional genes, including 43 tRNAs, 8 rRNAs, 76 protein-coding genes, and… More >

Riwa Mahai¹, Rongpeng Liu¹, Xiaolang Du¹, Zejing Mu¹, Xiaoyun Wang^1,*, Jun Yuan^2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.6, pp. 1203-1219, 2024, DOI:10.32604/phyton.2024.051559 - 27 June 2024

Abstract Rosaceae represents a vast and complex group of species, with its classification being intricate and contentious. The taxonomic placement of many species within this family has been a subject of ongoing debate. The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae. The cp genomes, varying in size from 153,366 to 159,895 bp, followed the typical quadripartite organization consisting of a large single-copy (LSC) region (84,545 to 87,883 bp), a small single-copy (SSC) region (18,174 to 19,259 bp), and a pair of inverted repeat (IR) regions (25,310 to… More >

Ji-Yang Zuo^1,2, Huan-Xin Chen^1,2, Zhi-Gang Liu^1,2, Qin Yang^1,2, Guo-Wei He^1,2,*

Congenital Heart Disease, Vol.18, No.1, pp. 7-21, 2023, DOI:10.32604/chd.2022.025451 - 09 January 2023

Abstract Background: Atrial septal defect (ASD) is one of the common congenital heart diseases. The MYH6 gene has a critical role in cardiac development but the role of MYH6 promoter variants in patients with ASD has not been explored. Methods: In 613 subjects including 320 ASD patients, we investigated the MYH6 gene promoter variants and verified the effect on gene expression by using cellular functional experiments and bioinformatics analysis. Results: Eleven variants were identified in the MYH6 gene promoter, of which four variants were found only in ASD patients, and two variants (g.3434G>C and g.4524C>T) were identified for the first… More > Graphic Abstract

Ahmad Ali AlZubi^*, Jazem Mutared Alanazi

Intelligent Automation & Soft Computing, Vol.35, No.3, pp. 3599-3611, 2023, DOI:10.32604/iasc.2023.027913 - 17 August 2022

Abstract Pathway reconstruction, which remains a primary goal for many investigations, requires accurate inference of gene interactions and causality. Non-coding RNA (ncRNA) is studied because it has a significant regulatory role in many plant and animal life activities, but interacting micro-RNA (miRNA) and long non-coding RNA (lncRNA) are more important. Their interactions not only aid in the in-depth research of genes’ biological roles, but also bring new ideas for illness detection and therapy, as well as plant genetic breeding. Biological investigations and classical machine learning methods are now used to predict miRNA-lncRNA interactions. Because biological identification… More >

Xiaolei Ding, Ruiwen Zhao, Sixi Lin, Jianren Ye^*

Phyton-International Journal of Experimental Botany, Vol.91, No.12, pp. 2813-2825, 2022, DOI:10.32604/phyton.2022.024609 - 29 August 2022

Abstract In Bazhong City, Sichuan Province, China, top dieback symptoms were found on many pine trees (Pinus thunbergii Parl). The tips of old needles first turned grayish-green and then developed into brown bands in the field. Phylogenetic analysis of concatenated ITS and EF1-α indicated the pathogen of this dieback disease as Diplodia neojuniperi. Additionally, effects of temperature, pH and medium on the mycelial growth were also characterized. The most favorable temperature and pH level for mycelial growth are 25°C and 8, respectively. The optimal medium for mycelial growth is PDA medium. To our knowledge, this is the first More >

Yujia Leng^1,#, Shuilian Wang^1,2,3,#, Ruoan Wang^2,#, Tao Tao¹, Shuwen Jia^1,2, Tao Song^2,3, Lina Xu^1,2, Xiuling Cai^1,2, Sukui Jin^1,2,*, Jiping Gao^1,2,4,*

Phyton-International Journal of Experimental Botany, Vol.91, No.5, pp. 943-958, 2022, DOI:10.32604/phyton.2022.018707 - 24 January 2022

Abstract Grain size traits are critical agronomic traits which directly determine grain yield, but the genetic bases of these traits are still not well understood. In this study, a total of 154 chromosome segment substitution lines (CSSLs) population derived from a cross between a japonica variety Koshihikari and an indica variety Nona Bokra was used to investigate grain length (GL), grain width (GW), length-width ratio (LWR), grain perimeter (GP), grain area (GA), and thousand grain weight (TGW) under four environments. QTL mapping analysis of six grain size traits was performed by QTL IciMapping 4.2 with an inclusive… More >

HUI-YING JIN^1,2, MAO-SONG PEI^1,2, DA-LONG GUO^1,2,*

BIOCELL, Vol.46, No.4, pp. 941-949, 2022, DOI:10.32604/biocell.2022.016718 - 15 December 2021

Abstract To understand the molecular characteristics of the miR477 gene family of grape (Vvi-miR477) and to predict its target genes, the Vvi-miR477 genes were identified from previous small RNA sequencing data, then phylogenetic analysis and prediction of target gene were conducted. The Vvi-miR477 family consists of two precursor sequences and three mature sequences. The miR477 family members were mostly 19-22nt in length. The sequence is relatively conservative. Vvi-MIR477a and Vvi-MIR477b are located on chromosomes 1 and 2, respectively. These precursor sequences can form the typical stable stem-loop structure. Their minimum folding free energy is −39.10 kcal/mol and −50.90 kcal/mol, More >