Purifying Selection Pressure Research Articles

New insights into the evolution analysis of trihelix gene family in eggplant (Solanum melongena L.) and expression analysis under abiotic stress.

Trihliex transcription factors (TFs) play crucial roles in plant growth and development, stress response, and plant hormone signaling network transmission. In order to comprehensively investigate the functions of trihliex genes in eggplant development and the abiotic stress response, we conducted an extensive analysis of the trihliex gene family in the eggplant genome. In this study, 30 trihelix gene family members were unevenly distributed on 12 chromosomes. On the basis of their phylogenetic relationships, these genes were conserved in different plant species and could be divided into six subfamilies, with trihelix genes within the same subfamily sharing similar structures. The promoter regions of trihelix genes contained cis-acting elements related to plant growth and development, plant hormones, and abiotic stress responses, suggesting potential applications in the development of more resistant crops. Selective pressure assessments indicated that trihliex genes have undergone purifying selection pressure. Expression analysis on the basis of transcriptomic profiles revealed that SmGT18, SmGT29, SmGT6, and SmGT28 are highly expressed in roots, leaves, flowers, and fruits, respectively. Expression analysis via quantitative real-time PCR (qRT‒PCR) revealed that most trihelix genes respond to low temperature, abscisic acid (ABA), and salicylic acid (SA), with SmGT29 exhibiting significant upregulation under cold stress conditions. The SmGT29 gene was subsequently successfully cloned from eggplant, which was located in the nucleus, robust transcriptional activity, and a protein molecular weight of 74.59kDa. On the basis of these findings, SmGT29 was postulated to be a pivotal candidate gene that actively responds to biotic stress stimuli, thereby supporting the plant's innate stress resistance mechanisms. In summary, this study was the first report on trihelix genes and their potential roles in eggplant plants. These results provided valuable insights for enhancing stress resistance and quality traits in eggplant breeding, thereby serving as a crucial reference for future improvement efforts.

Decrease in purifying selection pressures on wheat homoeologous genes: tetraploidization versus hexaploidization.

A series of polyploidizations in higher-order polyploids is the main event affecting gene content in a genome. Each polyploidization event can lead to massive functional divergence because of the subsequent decrease in selection pressure on duplicated genes; however, the causal relationship between multiple rounds of polyploidization and the functional divergence of duplicated genes is poorly understood. We focused on the Triticum-Aegilops complex lineage and compared selection pressure before and after tetraploidization and hexaploidization events. Although both events led to decreased selection pressure on homoeologous gene pairs (compared with diploids and tetraploids), the initial tetraploidization had a greater impact on selection pressure on homoeologous gene pairs than did subsequent hexaploidization. Consistent with this, selection pressure on expression patterns for the initial event relaxed more than those for the subsequent event. Surprisingly, the decreased selection pressure on these homoeologous genes was independent of the existence of in-paralogs within the same subgenome. Wheat homoeologous pairs had different evolutionary consequences compared with orthologs related to other mechanisms (ancient allopolyploidization, ancient autopolyploidization, and small-scale duplication). Furthermore, tetraploidization and hexaploidization also seemed to have different evolutionary consequences. This suggests that homoeologous genes retain unique functions, including functions that are unlikely to be preserved in genes generated by the other duplication mechanisms. We found that their unique functions differed between tetraploidization and hexaploidization (e.g., reproductive and chromosome segregation processes). These findings imply that the substantial number of gene pairs resulting from multiple allopolyploidization events, especially initial tetraploidization, may have been a unique source of functional divergence.

Genome-wide analysis and prediction of chloroplast and mitochondrial RNA editing sites of AGC gene family in cotton (Gossypium hirsutum L.) for abiotic stress tolerance

BackgroundCotton is one of the topmost fiber crops throughout the globe. During the last decade, abrupt changes in the climate resulted in drought, heat, and salinity. These stresses have seriously affected cotton production and significant losses all over the textile industry. The GhAGC kinase, a subfamily of AGC group and member of serine/threonine (Ser/Thr) protein kinases group and is highly conserved among eukaryotic organisms. The AGC kinases are compulsory elements of cell development, metabolic processes, and cell death in mammalian systems. The investigation of RNA editing sites within the organelle genomes of multicellular vascular plants, such as Gossypium hirsutum holds significant importance in understanding the regulation of gene expression at the post-transcriptional level.MethodsIn present work, we characterized twenty-eight GhAGC genes in cotton and constructed phylogenetic tree using nine different species from the most primitive to the most recent.ResultsIn sequence logos analyses, highly conserved amino acid residues were found in G. hirsutum, G. arboretum, G. raimondii and A. thaliana. The occurrence of cis-acting growth and stress-related elements in the promoter regions of GhAGCs highlight the significance of these factors in plant development and abiotic stress tolerance. Ka/Ks levels demonstrated that purifying selection pressure resulting from segmental events was applied to GhAGC with little functional divergence. We focused on identifying RNA editing sites in G. hirsutum organelles, specifically in the chloroplast and mitochondria, across all 28 AGC genes.ConclusionThe positive role of GhAGCs was explored by quantifying the expression in the plant tissues under abiotic stress. These findings help in understanding the role of GhAGC genes under abiotic stresses which may further be used in cotton breeding for the development of climate smart varieties in abruptly changing climate.

Genome-wide analysis of the MYB gene family and functional analysis of BhMYB79 in wax gourd

Wax gourd (Benincasa hispida) is an important cucurbit crop with economic and medicinal value. The myeloblastosis (MYB) gene family is one of the largest gene families in plants and regulates various biological processes, whereas the MYB gene family has not been systematically studied in wax gourd. In this study, we performed genome-wide identification of the MYB gene family in wax gourd and analyzed their phylogenetic relationship, MYB DNA-binding domain (MYB DBD), gene structure, protein motif, synteny, duplication mode and expression pattern. As a result, a total of 215 BhMYB genes (BhMYBs) were identified, belonging to four subfamilies: 1R-, 2R-, 3R- and 4R-MYB subfamilies. Genes of 1R-MYB subfamily and 2R-MYB subfamily were subdivided into different subgroups respectively. The analysis of MYB DBD, gene structure and protein motif showed that the most genes in the same subgroup have similar characteristics and the 2R-MYB genes were more conserved than the 1R-MYB genes. Interestingly, the long terminal retrotransposons (LTR-RTs) were found in the long introns of several BhMYBs. The results of synteny analysis showed that there were more syntenic gene pairs between wax gourd and other cucurbit crops, while the least number of syntenic gene pairs existed between wax gourd and rice. Gene duplication was the main reason for the expansion of the MYB gene family in wax gourd, with the transposed duplication (TRD) mode contributing more. All duplication BhMYB genes were under purifying selection pressure. Further expression analysis showed that many BhMYBs exhibited obvious tissue-specific expression and several BhMYBs were significantly induced by one or more abiotic stresses. BhMYB79 was particularly expressed in roots and significantly induced by salt, drought, cold and heat stresses, overexpression of which led to reduced tolerance to salt stress in Arabidopsis. In conclusion, our results provide a systematic analysis of wax gourd MYB gene family and facilitate the biological role study of BhMYB79 during wax gourd salt stress response process.

Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera).

Insectmitochondrial genomes(mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinaeand Aleyrodinae are characterized by intense purifying selection pressure.

Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.)

BackgroundMung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking.ResultsIn this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response.ConclusionsIn this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.

Identification of Bacteria and Viruses Associated with Patients with Acute Febrile Illness in Khon Kaen Province, Thailand.

The majority of cases of undifferentiated acute febrile illness (AFI) in the tropics have an undefined etiology. In Thailand, AFI accounts for two-thirds of illnesses reported to the Ministry of Public Health. To characterize the bacterial and viral causes of these AFIs, we conducted molecular pathogen screening and serological analyses in patients who sought treatment in Chum Phae Hospital, Khon Kaen province, during the period from 2015 to 2016. Through integrated approaches, we successfully identified the etiology in 25.5% of cases, with dengue virus infection being the most common cause, noted in 17% of the study population, followed by scrub typhus in 3.8% and rickettsioses in 6.8%. Further investigations targeting viruses in patients revealed the presence of Guadeloupe mosquito virus (GMV) in four patients without other pathogen co-infections. The characterization of four complete genome sequences of GMV amplified from AFI patients showed a 93-97% nucleotide sequence identity with GMV previously reported in mosquitoes. Nucleotide substitutions resulted in amino acid differences between GMV amplified from AFI patients and mosquitoes, observed in 37 positions. However, these changes had undergone purifying selection pressure and potentially had a minimal impact on protein function. Our study suggests that the GMV strains identified in the AFI patients are relatively similar to those previously reported in mosquitoes, highlighting their potential role associated with febrile illness.

Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses.

Plant protein phosphatase 2C (PP2C) plays vital roles in responding to various stresses, stimulating growth factors, phytohormones, and metabolic activities in many important plant species. However, the PP2C gene family has not been investigated in the economically valuable plant species sunflower (Helianthus annuus L.). This study used comprehensive bioinformatics tools to identify and characterize the PP2C gene family members in the sunflower genome (H. annuus r1.2). Additionally, we analyzed the expression profiles of these genes using RNA-seq data under four different stress conditions in both leaf and root tissues. A total of 121 PP2C genes were identified in the sunflower genome distributed unevenly across the 17 chromosomes, all containing the Type-2C phosphatase domain. HanPP2C genes are divided into 15 subgroups (A-L) based on phylogenetic tree analysis. Analyses of conserved domains, gene structures, and motifs revealed higher structural and functional similarities within various subgroups. Gene duplication and collinearity analysis showed that among the 53 HanPP2C gene pairs, 48 demonstrated segmental duplications under strong purifying selection pressure, with only five gene pairs showing tandem duplications. The abundant segmental duplication was observed compared to tandem duplication, which was the major factor underlying the dispersion of the PP2C gene family in sunflowers. Most HanPP2C proteins were localized in the nucleus, cytoplasm, and chloroplast. Among the 121 HanPP2C genes, we identified 71 miRNAs targeting 86 HanPP2C genes involved in plant developmental processes and response to abiotic stresses. By analyzing cis-elements, we identified 63 cis-regulatory elements in the promoter regions of HanPP2C genes associated with light responsiveness, tissue-specificity, phytohormone, and stress responses. Based on RNA-seq data from two sunflower tissues (leaf and root), 47 HanPP2C genes exhibited varying expression levels in leaf tissue, while 49 HanPP2C genes showed differential expression patterns in root tissue across all stress conditions. Transcriptome profiling revealed that nine HanPP2C genes (HanPP2C12, HanPP2C36, HanPP2C38, HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73) exhibited higher expression in leaf tissue, and five HanPP2C genes (HanPP2C13, HanPP2C47, HanPP2C48, HanPP2C54, and HanPP2C95) showed enhanced expression in root tissue in response to the four stress treatments, compared to the control conditions. These results suggest that these HanPP2C genes may be potential candidates for conferring tolerance to multiple stresses and further detailed characterization to elucidate their functions. From these candidates, 3D structures were predicted for six HanPP2C proteins (HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73), which provided satisfactory models. Our findings provide valuable insights into the PP2C gene family in the sunflower genome, which could play a crucial role in responding to various stresses. This information can be exploited in sunflower breeding programs to develop improved cultivars with increased abiotic stress tolerance.

Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance

BackgroundShewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis.ResultsPhylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The “open” genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer.ConclusionsThis study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals.

Integrative Analysis of the DUF668 Gene Family in Nicotiana tabacum to Excavate Their Potential Roles in Abiotic Stress Responses

The domain of the unknown function (DUF) gene families assumes pivotal roles in plant metabolic and stress responses. However, our comprehension of the tobacco DUF668 (NtDUF668) gene family and its specific reactions to heavy metal, drought, and salt stresses remain circumscribed. In the current investigation, a comprehensive genome-wide analysis of the NtDUF668 gene family was undertaken utilizing bioinformatics tools. The results unveiled a total of 20 members in the NtDUF668 gene family, denominated NtDUF668-01 to NtDUF668-20. Phylogenetic analyses indicated a closer genetic relationship of DUF668 genes between Nicotiana tabacum and Ipomoea batatas. The examination of gene structure and conservative motifs revealed a bifurcation into two major Clades, aligning with previous studies on DUF668 gene families from various plant species, emphasizing its highly conserved evolutionary mechanism across plants. The exploration of promoter regions of NtDUF668 genes revealed a plethora of cis-acting elements associated with abiotic and biotic stresses, light signaling, and phytohormones. Gene duplication events and selection pressure analysis disclosed the segmental duplication and strong purifying selection pressure during the evolution of NtDUF668 genes. Syntenic analysis indicated a relatively conserved evolutionary mechanism of DUF668 gene families within dicotyledons. Tissue-specific expression analysis suggested that NtDUF668 family members are potentially involved in root development, floral organ formation, and abscission. The expression patterns and qRT–PCR analysis of NtDUF668 genes implied the potentially functional involvements of NtDUF668s in response to multiple abiotic stresses. Furthermore, the stress-triggered member NtDUF668-08 exhibited specific nuclear localization. In conclusion, this genome-wide analysis illuminates the composition, phylogenetic relationships, and potential roles of the NtDUF668 gene family in abiotic stress responses. The identified candidate genes, particularly NtDUF668-08, warrant further research for functional investigation.

Molecular characterization and evolutionary relationships of DOFs in four cherry species and functional analysis in sweet cherry

The DOF (DNA binding with one finger) has multiple functions in plants. However, it has received little attention in the research field of cherries. In this study, the evolutionary relationship and molecular characterization of DOF in four cherry species were analyzed, revealing its expression pattern in sweet cherry. There are 23 members in Prunus avium cv. ‘Tieton’, 88 in Prunus cerasus, 53 in Cerasus × yedoensis, and 27 in Cerasus serrulata. Most of these genes are intron-less or non-intron, with a conserved C2-C2 domain. Due to heterozygosity and chromosomal ploidy, whole-genome duplication (WGD) events occur to varying degrees, and DOF genes are contracted during evolution. Furthermore, these genes are affected by purifying selection pressure. Under low-temperature treatment, the expression of PavDOF2 and PavDOF18 were significantly up-regulated, while that of PavDOF16 is significantly down-regulated. The expression of PavDOF9, PavDOF12, PavDOF14, PavDOF16, PavDOF17, PavDOF18, and PavDOF19 exhibits an increasing trend during flower development and varies during sweet cherry fruit development. PavDOF1, PavDOF8, PavDOF9, and PavDOF15 are localized in the nucleus but is not transcriptionally active. The findings systemically demonstrate the molecular characteristics of DOF in different cherry varieties, providing a basis for further research on the functions of these genes.

Genome-wide analysis of the peanut CaM/CML gene family reveals that the AhCML69 gene is associated with resistance to Ralstonia solanacearum

BackgroundCalmodulins (CaMs)/CaM-like proteins (CMLs) are crucial Ca2+-binding sensors that can decode and transduce Ca2+ signals during plant development and in response to various stimuli. The CaM/CML gene family has been characterized in many plant species, but this family has not yet been characterized and analyzed in peanut, especially for its functions in response to Ralstonia solanacearum. In this study, we performed a genome-wide analysis to analyze the CaM/CML genes and their functions in resistance to R. solanacearum.ResultsHere, 67, 72, and 214 CaM/CML genes were identified from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. The genes were divided into nine subgroups (Groups I-IX) with relatively conserved exon‒intron structures and motif compositions. Gene duplication, which included whole-genome duplication, tandem repeats, scattered repeats, and unconnected repeats, produced approximately 81 pairs of homologous genes in the AhCaM/CML gene family. Allopolyploidization was the main reason for the greater number of AhCaM/CML members. The nonsynonymous (Ka) versus synonymous (Ks) substitution rates (less than 1.0) suggested that all homologous pairs underwent intensive purifying selection pressure during evolution. AhCML69 was constitutively expressed in different tissues of peanut plants and was involved in the response to R. solanacearum infection. The AhCML69 protein was localized in the cytoplasm and nucleus. Transient overexpression of AhCML69 in tobacco leaves increased resistance to R. solanacearum infection and induced the expression of defense-related genes, suggesting that AhCML69 is a positive regulator of disease resistance.ConclusionsThis study provides the first comprehensive analysis of the AhCaM/CML gene family and potential genetic resources for the molecular design and breeding of peanut bacterial wilt resistance.

Genome-Wide Analysis of Pentatricopeptide Repeat Gene Family in Peanut and Identification of AhPPR598 Resistance to Ralstonia solanacearum

Pentatricopeptide repeat (PPR) proteins, with tandem 30–40 amino acids, were characterized as one kind of nucleus coding protein. They have been demonstrated to play important roles in RNA editing, plant growth and development, and plant immunity. Although the PPR gene family has been characterized in some plant species, less is known about this family in peanut, especially their functions in response to Ralstonia solanacearum. In this study, we performed a genome-wide analysis to identify PPR genes and their functions in resistance to R. solanacearum. Here, 389, 481, and 1079 PPR genes were identified from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. Allopolyploidization was the main reason for the increased number of the AhPPR members. Gene duplication brought about 367 pairs of homologous genes of PPRs in A. hypogaea. Whole-genome replication, tandem repeats, scattered repeats, and unconnected repeats constituted the replication types. The substitution rates of nonsynonymous (Ka) versus synonymous (Ks) of all homologous pairs were less than 1.0, suggesting that the homologous AhPPRs underwent intense purifying selection pressure and remained conserved in both structure and function. RNA-seq and RT-qPCR analyses showed that AhPPR598 gene was highly expressed in the aerial part of peanut and involved in response to R. solanacearum. The transient expression of AhPPR598 in Nicotiana benthamiana induced the HR-mediated cell death, up-regulated expression of resistant marker genes, and enhanced the resistance to R. solanacearum, suggesting AhPPR598 was a positive regulator of immunity by regulating the JA and SA pathways. These results provide a new understanding of the origin, distribution, and evolution of the AhPPR gene family and potential gene resources for peanut-resistant breeding.

Genome-wide identification and expression profiling of photosystem II (PsbX) gene family in upland cotton (Gossypium hirsutum L)

BackgroundPhotosystem II (PSII) constitutes an intricate assembly of protein pigments, featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane. The low-molecular-weight transmembrane protein PsbX has been identified in PSII, which is associated with the oxygen-evolving complex. The expression of PsbX gene protein is regulated by light. PsbX's central role involves the regulation of PSII, facilitating the binding of quinone molecules to the Qb (PsbA) site, and it additionally plays a crucial role in optimizing the efficiency of photosynthesis. Despite these insights, a comprehensive understanding of the PsbX gene's functions has remained elusive.ResultsIn this study, we identified ten PsbX genes in Gossypium hirsutum L. The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade. The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species. Furthermore, the orthologous/paralogous, Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence, which resulted in the whole genome and segmental duplication. The expression patterns of GhPsbX genes exhibited variations across specific tissues, as indicated by the analysis. Moreover, the expression of GhPsbX genes could potentially be regulated in response to salt, intense light, and drought stresses. Therefore, GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions.ConclusionWe examined the structure and function of PsbX gene family very first by using comparative genomics and systems biology approaches in cotton. It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions. Collectively, the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.

Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea

The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3′-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses.

Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress.

Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production.

Assembly and comparative analysis of the complete mitochondrial genome of Trigonella foenum-graecum L.

BackgroundTrigonella foenum-graecum L. is a Leguminosae plant, and the stems, leaves, and seeds of this plant are rich in chemical components that are of high research value. The chloroplast (cp) genome of T. foenum-graecum has been reported, but the mitochondrial (mt) genome remains unexplored.ResultsIn this study, we used second- and third-generation sequencing methods, which have the dual advantage of combining high accuracy and longer read length. The results showed that the mt genome of T. foenum-graecum was 345,604 bp in length and 45.28% in GC content. There were 59 genes, including: 33 protein-coding genes (PCGs), 21 tRNA genes, 4 rRNA genes and 1 pseudo gene. Among them, 11 genes contained introns. The mt genome codons of T. foenum-graecum had a significant A/T preference. A total of 202 dispersed repetitive sequences, 96 simple repetitive sequences (SSRs) and 19 tandem repetitive sequences were detected. Nucleotide diversity (Pi) analysis counted the variation in each gene, with atp6 being the most notable. Both synteny and phylogenetic analyses showed close genetic relationship among Trifolium pratense, Trifolium meduseum, Trifolium grandiflorum, Trifolium aureum, Medicago truncatula and T. foenum-graecum. Notably, in the phylogenetic tree, Medicago truncatula demonstrated the highest level of genetic relatedness to T. foenum-graecum, with a strong support value of 100%. The interspecies non-synonymous substitutions (Ka)/synonymous substitutions (Ks) results showed that 23 PCGs had Ka/Ks < 1, indicating that these genes would continue to evolve under purifying selection pressure. In addition, setting the similarity at 70%, 23 homologous sequences were found in the mt genome of T. foenum-graecum.ConclusionsThis study explores the mt genome sequence information of T. foenum-graecum and complements our knowledge of the phylogenetic diversity of Leguminosae plants.

ORFans in Mitochondrial Genomes of Marine Polychaete Polydora.

Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three "ORFan" regions (544, 1,060, and 427 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication.

Genome-wide identification of bZIP gene family and expression analysis of BhbZIP58 under heat stress in wax gourd

BackgroundThe basic leucine zipper (bZIP) transcription factor family is one of the most abundant and evolutionarily conserved gene families in plants. It assumes crucial functions in the life cycle of plants, including pathogen defense, secondary metabolism, stress response, seed maturation, and flower development. Although the genome of wax gourd has been published, little is known about the functions, evolutionary background, and gene expression patterns of the bZIP gene family, which limits its utilization.ResultsA total of 61 bZIP genes (BhbZIPs) were identified from wax gourd (Benincasa hispida) genome and divided into 12 subgroups. Whole-genome duplication (WGD) and dispersed duplication (DSD) were the main driving forces of bZIP gene family expansion in wax gourd, and this family may have undergone intense purifying selection pressure during the evolutionary process. We selected BhbZIP58, only one in the member of subgroup B, to study its expression patterns under different stresses, including heat, salt, drought, cold stress, and ABA treatment. Surprisingly, BhbZIP58 had a dramatic response under heat stress. BhbZIP58 showed the highest expression level in the root compared with leaves, stem, stamen, pistil, and ovary. In addition, BhbZIP58 protein was located in the nucleus and had transcriptional activation activity. Overexpression of BhbZIP58 in Arabidopsis enhanced their heat tolerance.ConclusionsIn this study, bZIP gene family is systematically bioinformatically in wax gourd for the first time. Particularly, BhbZIP58 may have an important role in heat stress. It will facilitate further research on the bZIP gene family regarding their evolutionary history and biological functions.