Genome-Wide Analysis of Flax (Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors

Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17 LuGRF genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17 LuGRFs (88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades; LuGRF genes were found in four clades. Most LuGRF gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of LuGRF genes were also analyzed. The three-dimensional structure of LuGRF proteins was predicted using homology modeling. The transcript expression data indicated that most LuGRF family members were highly expressed in flax fruit and embryos, whereas LuGRF3, LuGRF12 and LuGRF16 were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both LuGRF1 and LuGRF11 were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense. LuGRF1 was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of LuGRF gene function and obtaining improved flax breeding lines.

The complete mitogenome of the Mugil cephalus (Mugiliformes: Mugilidae) from the Yellow Sea, China

Mugil cephalus Linnaeus, 1758 is a teleost fish widely distributed in coastal waters that plays an important role in commercial fisheries. In the present study, the complete mitogenome of M. cephalus from the Yellow Sea, China, was sequenced using Illumina Novaseq sequencing. The mitogenome of the M. cephalus was 16,744 bases in length (GenBank accession No. ON262567) including 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and a D-loop control region. The overall base composition of the genome was 28.2% A, 29.5% C, 26.9% T, and 15.4% G. The analysis of genetic similarity and phylogenetic relationship of M. cephalus from different geographic regions of the world indicated that the species from the Yellow Sea was most similar to NWP1 which is one of the three cryptic species of M. cephalus in Northwestern Pacific.

A Comprehensive Analysis of the Fowleria variegata (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae

Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using high-throughput Illumina sequencing. Through a comparative mitogenomic analysis, F. variegate was shown to exhibit a typical genome architecture and composition, including 13 protein-coding, 22 tRNA and 2 rRNA genes and a control region, consistent with studies of other Apogonidae species. Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. Phylogenetic reconstruction based on maximum likelihood and Bayesian approaches provided robust evidence that F. variegata forms a basal lineage closely related to P. trimaculatus within Apogonidae, offering novel perspectives into the molecular evolution of this family. By generating new mitogenomic resources and evolutionary insights, this study makes important headway in elucidating the phylogenetic relationships and mitogenomic characteristics of Apogonidae fishes. The findings provide critical groundwork for future investigations into the drivers of diversification, speciation patterns, and adaptive radiation underlying the extensive ecological diversity and biological success of these marine fishes using phylogenomics and population genomics approaches.

Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato

The PLATZ (plant AT protein and zinc-binding protein) transcription factor family is involved in the regulation of plant growth and development and plant stress response. In this study, 24 SlPLATZs were identified from the cultivated tomato genome and classified into four groups based on the similarity of conserved patterns among members of the same subfamily. Fragment duplication was an important way to expand the SlPLATZ gene family in tomatoes, and the sequential order of tomato PLATZ genes in the evolution of monocotyledonous and dicotyledonous plants and the roles they played were hypothesized. Expression profiles based on quantitative real-time reverse transcription PCR showed that SlPLATZ was involved in the growth of different tissues in tomatoes. SlPLATZ21 acts mainly in the leaves. SlPLATZ9, SlPLATZ21, and SlPLATZ23 were primarily involved in the red ripening, expanding, and mature green periods of fruit, respectively. In addition, SlPLATZ1 was found to play an important role in salt stress. This study will lay the foundation for the analysis of the biological functions of SlPLATZ genes and will also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation.

A Comprehensive Analysis of Triplophysa labiata (Kessler, 1874) Mitogenome and Its Phylogenetic Implications within the Triplophysa Genus

In order to resolve the long-standing controversy surrounding the relationships within the Triplophysa genus, we conducted an extensive analysis of the complete mitogenome of Triplophysa labiata using DNBSEQ short reads. Additionally, we reconstructed the phylogeny of the Nemacheilidae family using mitogenome data. By comparing all available mitogenomes within the Triplophysa genus, we gained valuable insights into its evolutionary history. Our findings revealed that the mitogenome sequence of T. labiata is circular, spanning a length of 16,573 bp. It encompasses 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (D-loop). Among the PCGs, the start codon ATG was commonly observed, except in cox1, while the stop codons TAA/TAG/T were found in all PCGs. Furthermore, purifying selection was evident across all PCGs. Utilizing maximum likelihood (ML) methods, we employed the 13 PCGs and the concatenated nucleotide sequences of 30 Triplophysa mitogenomes to infer the phylogeny. Our results strongly supported the division of the Triplophysa genus into four primary clades. Notably, our study provides the first evidence of the close relationship between T. labiata and T. dorsalis. These findings serve as a significant foundation for future investigations into the mitogenomics and phylogeny of Nemacheilidae fishes, paving the way for further advancements in this field of research.

Comparative transcriptomic analysis reveals differences in MADS-box genes of different hypericum in Changbai Mountains

To explore the differences between the hypericum in the Changbai Mountains, we carried out a transcriptome analysis of two common hypericums in the area, which was Hypericum attenuatum Choisy and Hypericum longistylum Oliv. We screened the MADS-box genes to analyze divergence time and evolutionary selection expression, and determine their expression levels. The results showed that we detected 9287 differentially expressed genes in the two species, of which shared 6044 genes by the two species. Analysis of the selected MADS genes revealed that the species was in an environment adapted to its natural evolution. The divergence time estimation showed that the segregation of these genes in the two species was related to the changes of external environment and genome replication events. The results of relative expression showed that the later flowering period of Hypericum attenuatum Choisy was related to the higher expression of the SVP (SHORT VEGETATIVE PHASE) and the AGL12 (AGAMOUS LIKE 12), while the lower expression of the FUL (FRUITFULL).

Identification, Molecular Characteristics, and Evolution of YABBY Gene Family in Melastoma dodecandrum

The YABBY gene family plays an important role in plant growth and development, such as response to abiotic stress and lateral organ development. YABBY TFs are well studied in numerous plant species, but no study has performed a genome-wide investigation of the YABBY gene family in Melastoma dodecandrum. Therefore, a genome-wide comparative analysis of the YABBY gene family was performed to study their sequence structures, cis-acting elements, phylogenetics, expression, chromosome locations, collinearity analysis, protein interaction, and subcellular localization analysis. A total of nine YABBY genes were found, and they were further divided into four subgroups based on the phylogenetic tree. The genes in the same clade of phylogenetic tree had the same structure. The cis-element analysis showed that MdYABBY genes were involved in various biological processes, such as cell cycle regulation, meristem expression, responses to low temperature, and hormone signaling. MdYABBYs were unevenly distributed on chromosomes. The transcriptomic data and real-time reverse transcription quantitative PCR (RT-qPCR) expression pattern analyses showed that MdYABBY genes were involved in organ development and differentiation of M. dodecandrum, and some MdYABBYs in the subfamily may have function differentiation. The RT-qPCR analysis showed high expression of flower bud and medium flower. Moreover, all MdYABBYs were localized in the nucleus. Therefore, this study provides a theoretical basis for the functional analysis of YABBY genes in M. dodecandrum.

De novogenomic analysis ofEnterobacter asburiaeEBRJ12, a plant growth-promoting rhizobacteria isolated from the rhizosphere of Phaseolus vulgarisL

AIM

Environmental stresses such as water deficit induced stress are one of the major limiting factors in crop production. However, some plant growth-promoting rhizobacteria (PGPR) can promote plant growth in such adverse condition. Therefore, the objective was to isolate rhizospheric bacteria from Phaseolus vulgaris L. growing in a drought-affected soil and to analyze its plant growth promoting (PGP) efficacy to black gram (Vigna mungo L.) and Bhut jolokia (Capsicum chinense Jacq.). Whole-genome sequencing of the potential bacteria was targeted to analyze the genetic potential of the isolate as a plant growth-promoting agent.

METHODS AND RESULTS

The isolate Enterobacter asburiae EBRJ12 was selected based on its PGP efficacy, which significantly improved plant growth and development. The genomic analysis revealed the presence of one circular chromosome of size 4.8 Mb containing 16 genes for osmotic stress regulation including osmotically inducible protein osmY, outer membrane protein A precursor ompA, aquaporin Z, and an operon for osmoprotectant ABC transporter yehZYXW. Moreover, the genome has a complete genetic cluster for biosynthesis of siderophore Enterobactin and siderophore Aerobactin.The PGP effects were verified with black gram and Bhut jolokia in pot experiments. The isolate significantly increased the shoot length by 35.0% and root length by 58.0% of black gram, while 41.0% and 57.0% of elevation in shoot and root length were observed in Bhut jolokia compared to non-inoculated plants.

CONCLUSIONS

The EBRJ12 has PGP features that could improve the growth in host plants, and the genomic characterization revealed the presence of genetic potential for plant growth promotion.

Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple (Ananas comosus)

Background

Pineapple is the only commercially grown fruit crop in the Bromeliaceae family and has significant agricultural, industrial, economic, and ornamental value. GRF (growth-regulating factor) proteins are important transcription factors that have evolved in seed plants (embryophytes). They contain two conserved domains, QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys), and regulate multiple aspects of plant growth and stress response, including floral organ development, leaf growth, and hormone responses. The GRF family has been characterized in a number of plant species, but little is known about this family in pineapple and other bromeliads.

Main discoveries

We identified eight GRF transcription factor genes in pineapple, and phylogenetic analysis placed them into five subfamilies (I, III, IV, V, VI). Segmental duplication appeared to be the major contributor to expansion of the AcGRF family, and the family has undergone strong purifying selection during evolution. Relative to that of other gene families, the gene structure of the GRF family showed less conservation. Analysis of promoter cis-elements suggested that AcGRF genes are widely involved in plant growth and development. Transcriptome data and qRT-PCR results showed that, with the exception of AcGRF5, the AcGRFs were preferentially expressed in the early stage of floral organ development and AcGRF2 was strongly expressed in ovules. Gibberellin treatment significantly induced AcGRF7/8 expression, suggesting that these two genes may be involved in the molecular regulatory pathway by which gibberellin promotes pineapple fruit expansion.

Conclusion

AcGRF proteins appear to play a role in the regulation of floral organ development and the response to gibberellin. The information reported here provides a foundation for further study of the functions of AcGRF genes and the traits they regulate.

Genomic characterization and expression analysis of TCP transcription factors in Setaria italica and Setaria viridis

The plant-specific TCP transcription factor plays important roles in plant development and environment adaptation. Setaria italica and Setaria viridis, the C4 model plants, can grow on drought or arid soils. However, there is no systematic information about the genomic dissection and the expression of Setaria TCP genes. A total of 22 TCP genes were both identified from S. italica and S. viridis genomes. They all contained bHLH domain and were grouped into three main clades (PCF, CIN, and CYC/TB1). The TCP genes in the same clades shared similar gene structures. Cis-element in the TCP promoter regions were analyzed and associated with hormones and stress responsiveness. Ten TCP genes were predicted to be targets of miRNA319. Moreover, gene ontology analysis indicated three SiTCP and three SvTCP genes were involved in the regulation of shoot development, and SiTCP16/SvTCP16 were clustered together with tillering controlling gene TB1. The TCP genes were differentially expressed in the organs, but SiTCP/SvTCP orthologs shared similar expression patterns. Ten SiTCP members were downregulated under drought or salinity stresses, indicating they may play regulatory roles in abiotic stresses. The study provides detailed information regarding Setaria TCP genes, providing the theoretical basis for agricultural applications.

Identification and Analysis of MYB Gene Family for Discovering Potential Regulators Responding to Abiotic Stresses in Curcuma wenyujin

MYB superfamily is one of the most abundant families in plants, and plays critical role in plant growth, development, metabolism regulation, and stress response. Curcuma wenyujin is the main source plant of three traditional Chinese medicines, which are widely used in clinical treatment due to its diverse pharmacological activities. In present study, 88 CwMYBs were identified and analyzed in C. wenyujin, including 43 MYB-related genes, 42 R2R3-MYB genes, two 3R-MYB genes, and one 4R-MYB gene. Forty-three MYB-related proteins were classified into several types based on conserved domains and specific motifs, including CCA1-like type, R-R type, Myb-CC type, GARP-like type, and TBR-like type. The analysis of motifs in MYB DBD and no-MYB regions revealed the relevance of protein structure and function. Comparative phylogeny analysis divided 42 R2R3-MYB proteins into 19 subgroups and provided a reference for understanding the functions of some CwMYBs based on orthologs of previously characterized MYBs. Expression profile analysis of CwMYB genes revealed the differentially expressed genes responding to various abiotic stresses. Four candidate MYB genes were identified by combining the results of phylogeny analysis and expression analysis. CwMYB10, CwMYB18, CwMYB39, and CwMYB41 were significantly induced by cold, NaCl, and MeJA stress treatments. CwMYB18 and CwMYB41 were proved as regulators with activity of transcriptional activation, whereas CwMYB39 and CwMYB10 were not. They may participate in the response to abiotic stresses through different mechanisms in C. wenyujin. This study was the first step toward understanding the CwMYB family and the response to abiotic stresses in C. wenyujin.

Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance

Plant-specific TCP transcription factors play a key role in plant development and stress responses. Chrysanthemum nankingense shows higher cold tolerance than its ornamental polyploid counterpart. However, whether the TCP gene family plays a role in conferring cold tolerance upon C. nankingense remains unknown. Here, we identified 23 CnTCP genes in C. nankingense, systematically analyzed their phylogenetic relationships and synteny with TCPs from other species, and evaluated their expression profiles at low temperature. Phylogenetic analysis of the protein sequences suggested that CnTCP proteins fall into two classes and three clades, with a typical bHLH domain. However, differences between C. nankingense and Arabidopsis in predicted protein structure and binding sites suggested a unique function of CnTCPs in C. nankingense. Furthermore, expression profiles showed that expression of most CnTCPs were downregulated under cold conditions, suggesting their importance in plant responses to cold stress. Notably, expression of miR319 and of its predicted target genes, CnTCP2/4/14, led to fast responses to cold. Overexpression of Arabidopsis CnTCP4 led to hypersensitivity to cold, suggesting that CnTCP4 might play a negative role in C. nankingense responses to cold stress. Our results provide a foundation for future functional genomic studies on this gene family in chrysanthemum.

Complete chloroplast genome sequence of Dendranthema zawadskii Herbich

Dendranthema zawadskii Herbich is one of 17 species of Dendranthema in China, and it is often used as an ornamental plant. The chloroplast genome size of Dendranthema zawadskii Herbich is 150,995 bp, including a large single-copy region (82,771 bp), a small single-copy region (18,308 bp), and a pair of inverted repeats regions (24,958 bp). Total 112 genes were annotated, including 79 protein-coding genes, four ribosomal RNA genes, and 29 transfer RNA genes. The phylogenetic position of Dendranthema zawadskii Herbich is close to Dendranthema indicum.

A New Method for Next-Generation Sequencing of the Full Hepatitis B Virus Genome from A Clinical Specimen: Impact for Virus Genotyping

Hepatitis B virus (HBV) is an enveloped virus that induces chronic liver disease. HBV has been classified into eight genotypes (A–H) according to its genome sequence by using Sanger sequencing or reverse hybridization. Sanger sequencing is often restricted to analyzing the S gene and is inaccurate for detecting minority genetic variants, whereas reverse hybridization detects only known mutations. Next-generation sequencing (NGS) is a robust tool for clinical virology with different protocols available. The objective of this study was to develop a new method for the study of viral genetic polymorphisms or more accurate genotyping using genome amplification followed by NGS. Plasma obtained from five chronically infected HBV individuals was used for viral DNA isolation. HBV full-genome PCR amplification was the enrichment method for NGS. Primers were used to amplify all HBV genotypes in three overlapping amplicons, following a tagmentation step and Illumina NGS. For phylogenetic analysis, sequences were extracted from the HBVdb database. We were able to amplify a full HBV genome; further, NGS was shown to be a robust method and allowed better genotyping, mainly in patients carrying mixed genotypes, classified according to other techniques. This new method may be significant for whole genome analyses, including other viruses.

The complete mitochondrial genome of the hydrozoan jellyfish Spirocodon saltatrix (Cnidaria; Hydrozoa; Anthoathecata) with phylogeny analysis

In the present study, we sequenced and analyzed the complete mitochondrial genome of the hydrozoan jellyfish Spirocodon saltatrix. The mitochondrial genome was a linear form (15,752 bp long, 70.4% AT), consisting of 13 protein coding genes (cox1, cox2, atp8, atp6, cox3, nad2, nad5, nad6, nad3, nad4L, nad1, nad4, and cytB), two tRNAs (tRNA-Met and tRNA-Trp), and two rRNAs (12S and 16S). Mitochondrial gene arrangement of the S. saltatrix was completely identical to already-known mitochondrial genomes of hydrozoans. Molecular phylogenetic analysis using 13 protein-coding genes showed that S. saltatrix was closely related to the hydrozoan Clava multicornis.

The Cytochrome P450 Monooxygenase Inventory of Grapevine (Vitis vinifera L.): Genome-Wide Identification, Evolutionary Characterization and Expression Analysis

The cytochrome P450 (CYP) monooxygenase superfamily, belonging to heme-thiolate protein products, plays a vital role in metabolizing physiologically valuable compounds in plants. To date, CYP superfamily genes have not yet been characterized in grapevine (V. vinifera L.), and their functions remain unclear. In this study, a sum of 236 VvCYPs, divided into 46 families and clustered into nine clans, have been identified based on bioinformatics analyses in grapevine genome. The characteristics of both exon-intron organizations and motif structures further supported the close evolutionary relationships of VvCYP superfamily as well as the reliability of phylogenetic analysis. The gene number-based hierarchical cluster of CYP subfamilies of different plants demonstrated that the loss of CYP families seems to be limited to single species or single taxa. Promoter analysis elucidated various cis-regulatory elements related to phytohormone signaling, plant growth and development, as well as abiotic/biotic stress responses. The tandem duplication mainly contributed to the expansion of the VvCYP superfamily, followed by singleton duplication in grapevine. Global RNA-sequencing data of grapevine showed functional divergence of VvCYPs as diverse expression patterns of VvCYPs in various organs, tissues, and developmental phases, which were confirmed by quantitative real-time reverse transcription PCR (qRT-PCR). Taken together, our results provided valuable inventory for understanding the classification and biological functions of the VvCYPs and paved the way for further functional verification of these VvCYPs and are helpful to grapevine molecular breeding.

Genome-Wide Identification, Characterization, and Transcript Analysis of the TCP Transcription Factors in Vitis vinifera

The TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS (TCP) protein, belonging to a plant-specific transcription factors (TFs) family, participates in the control of plant growth and development by regulating cell proliferation. Until now, a comprehensive study of concerning the TCP gene family and their roles in grapevine (Vitis vinifera L.) has not been completed. Using bioinformatics approaches, 17 VvTCP genes were identified and further classified into two classes, designated class I (PCF subclass) and class II (CIN and CYC/TB1 subclass), which was further supported by exon-intron organizations and conserved motif analysis. Promoter analysis demonstrated that VvTCPs have numerous cis-acting elements related to plant growth and development, phytohormone, and abiotic/biotic stress responses. The singleton duplication of grapevine TCP genes contributed to this gene family expansion. The syntenic analyses among Vitis vinifera, Arabidopsis, and Oryza sativa showed that these genes located in corresponding syntenic blocks arose before the divergence of V. vinifera, Arabidopsis, and O. sativa. The expression levels of 17 VvTCPs were determined in different tissues and fruit developmental stages, and abscisic acid (ABA) treatment. Seventeen VvTCPs exhibited distinct tissue-specific expression patterns, potentially illustrating the functional divergence of VvTCPs in all tested tissues. Eleven VvTCPs were down-regulated in five berry developmental stages, while three VvTCPs were up-regulated. Additionally, many members were strongly modulated by ABA treatment, suggesting these VvTCPs have important and diverse regulatory roles in ABA treatment. Our results provide valuable information on the evolution and functions of the VvTCPs, pave the way for further functional verification of these VvTCPs in grapevine.

The complete chloroplast genome sequence of Chimonanthus praecox cv. concolor

Calycanthaceae is a perennial shrub endemic to China with important ornamental and medicinal values. In this study, Chimonanthus praecox cv. concolor chloroplast (cp) genome was characterized using Illumina paired-end reads data. In total, whole cp genome is 153,254 bp long and contains a small single-copy region of 19,769 bp, a pair of repeat (IRa and IRb) regions of 23,286 bp each, and a large single-copy region of 86,913 bp. This genome contains 129 genes, including 84 protein-genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis based on 19 cp genomes showed that C. praecox cv. concolor is closely related to Chimonanthus praecox and Chimonanthus nitens.

Characterization of the complete mitochondrial genome of Pelteobagrus intermedius (Nichols et Pope)

Pelteobagrus intermedius is a unique freshwater fish native species in the Hainan Island and Guangxi and other water systems of China. In this study, the complete mitochondrial genome sequence of P. intermedius was determined from whole genome Illumina sequencing data. The total length of the mtDNA was 16,532 bp, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region. Phylogenetic analysis suggested that the P. intermedius is closely related to Tachysurus fulvidraco. The results will serve as a helpful reference for further studies on the conservation genetics of genus Pelteobagrus.

RNA-dependent RNA polymerase: Addressing Zika outbreak by a phylogeny-based drug target study

Since the first major outbreak of Zika virus (ZIKV) in 2007, ZIKV is spreading explosively through South and Central America, and recent reports in highly populated developing countries alarm the possibility of a more catastrophic outbreak. ZIKV infection in pregnant women leads to embryonic microcephaly and Guillain-Barré syndrome in adults. At present, there is limited understanding of the infectious mechanism, and no approved therapy has been reported. Despite the withdrawal of public health emergency, the WHO still considers the ZIKV as a highly significant and long-term public health challenge that the situation has to be addressed rapidly. Non-structural protein 5 is essential for capping and replication of viral RNA and comprises a methyltransferase and RNA-dependent RNA polymerase (RdRp) domain. We used molecular modeling to obtain the structure of ZIKV RdRp, and by molecular docking and phylogeny analysis, we here demonstrate the potential sites for drug screening. Two metal binding sites and an NS3-interacting region in ZIKV RdRp are demonstrated as potential drug screening sites. The docked structures reveal a remarkable degree of conservation at the substrate binding site and the potential drug screening sites. A phylogeny-based approach is provided for an emergency preparedness, where similar class of ligands could target phylogenetically related proteins.

Genetic diversity and phylogenetic relationships of seven Amorphophallus species in southwestern China revealed by chloroplast DNA sequences

Plants species in the genus Amorphophallus are of great economic importance, as they are the only plants known to produce glucomannan. Although southwestern China has been recognized as one of the origin centres of Amorphophallus, only a few studies assessing its genetic diversity have been reported. To aid in the utilization and conservation of Amorphophallus species, we evaluated the genetic diversity and phylogenetic relationships among seven edible Amorphophallus species using three chloroplast DNA regions (rbcL, trnL and trnK-matK). The results showed that the genetic diversity at the population level was relatively low, with over half of the populations harbouring only one haplotype. The widely scattered species, A. konjac, had the largest genetic diversity, while the narrow endemic species, A. yuloensis, possessed only one haplotype. Phylogeny analysis identified three well-supported major lineages. Our study suggested that habitat fragmentation might be a driver of the genetic variation patterns within and between populations of Amorphophallus. A conservation strategy consisting of in situ conservation and germplasm collection is recommended.

Sequencing and analysis of the complete mitochondrial genome of Hippocampus spinosissimus Weber, 1913 (Gasterosteiformes: Syngnathidae)

abtract The complete mitochondrial genome of the Hedgehog Seahorse (Hippocampus spinosissimus) is 16 530 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene organization of H. spinosissimus was similar to that observed in most vertebrate creatures. All protein-coding genes use the typical initiation codon ATG, except for COX1 that uses GTG. The overall base composition of H. spinosissimus is 32.2% for A, 22.72% for C, 30.19% for T, and 14.89% for G, with a slight AT bias of 62.39%. Hippocampus spinosissimus showed a closer genetic relationship with H. kelloggi according to the phylogenetic analysis.

Complete mitochondrial genome of Tlacuatzin canescens (Grayish Mouse Opossum)

In this study, we report the complete mitochondrial genome of the Grayish Mouse Opossumm, Tlacuatzin canescens. The mitochondrial genome is 16 460 bp in length and has a base composition of A (35.7%), T (31.3%), C (21.3%), and G (11.7%), demonstrating an obvious bias of high AT content (67%). The mitochondrial genome contains a typically conserved structure, encoding 13 protein-coding genes (PCGs), 20 transfer RNA genes (tRNA), 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and a control region (D-loop region). Except for ND6 gene, all other PCGs were located on the H-strand. ND4 gene and ND4L gene were overlapped by 4 bp, and ATP8 gene and ATP6 gene were overlapped by 45 bp. The nucleotide sequence of 13 PCGs of T. canescens and other 30 Didelphimorphia species were used for phylogenetic analysis. The result indicated T. canescens a relative close relationship with species Monodelphis domestica.

Complete mitochondrial genome of the great seahorse Hippocampus kelloggi Jordan & Snyder, 1901 (Gasterosteiformes: Syngnathidae)

In this study, the complete mitogenome sequence of great seahorse Hippocampus kelloggi (Gasterosteiformes: Syngnathidae) has been amplified and sequenced employing the polymerase chain reaction-based method. The total length of mitochondrial DNA is 16 536 bp and includes 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of H. kelloggi was similar to that observed in most vertebrate creatures. The overall base composition of H. kelloggi is 32.19% for A, 23.68% for C, 29.30% for T, and 14.82% for G, with a slight AT bias of 61.49%. Phylogenetic analyses based on complete mitochondrial genome sequence showed that H. kelloggi has a close genetic relationship to H. reidi, H. ingens, and H. kuda.

Complete mitochondrial genome of Aulonocara stuartgranti (Flavescent peacock cichlid)

In this study, the complete mitochondrial genome of the flavescent peacock cichlid Aulonocara stuartgranti was determined. The mitochondrial genome is 16 669 bp in length, and encodes 1 D-loop region, 2 ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. Average GC content of this genome is 45.8%. ATP8 and ATP6 genes overlap by nine nucleotides, ND5 and ND6 genes by four nucleotides, and ND4L and ND4 genes share six nucleotides. All coding genes use ATG as start codon with except COX1 initiating with GTG. The phylogenetic tree involving 22 available closely related species further validated the newly determined sequences and phylogeny of A. stuartgranti.

Complete mitochondrial genome of Rhynchophorus ferrugineus

In this study, we determined the mitochondrial genome of Rhynchophorus ferrugineus. The mitochondrial genome is 15 924 bp in length (GC content: 25.6%), encodes 2 ribosomal RNA genes, 13 protein-coding genes, 21 transfer RNA genes, and 1 D-loop region. nad6 and cob are overlapped by 30 bp and atp8 and atp6 are overlapped by 12 bp. The phylogenetic tree involving 29 available closely related species further validated the new determined sequences and phylogeny of R. ferrugineus.

Complete mitochondrial genome of the argentine ant, Linepithema humile (Hymenoptera: Formicidae)

In this study, the complete mitochondrial genome of the widespread invasive Argentine ant (Linepithema humile) was first determined. The mitochondrial genome is 16 098 bp in length, and encodes one D-loop region, two ribosomal RNA genes, 13 protein-coding genes, and 18 transfer RNA genes. Average GC content of this genome is 19.68%. nad6 and cob genes were overlapped by 4 bp. The phylogenetic tree involving 13 available closely related species further validated the new determined sequences and phylogeny of L. humile.

The complete mitochondrial genome of Tambocerus sp. (Hemiptera: Cicadellidae)

The complete mitochondrial genome of Tambocerus sp. (Hemiptera: Cicadellidae) from Zhejiang and Anhui provinces of China was sequenced. The total length of the mitogenome is 15 955 bp (GenBank accession no. KT827824) and consists of 22 transfer RNAs, 13 protein-coding genes, 2 ribosomal RNAs and 1 control region. The base composition of the heavy strand for A, T, C, and G is 41.39, 35.02, 14.00, and 9.59%, respectively. All of the protein-coding genes (PCGs) start with ATN. Five protein-coding genes use TAA as stop codons, four use TAG as stop codons, and others use incomplete stop codons ''T--'' or ''TA-''. The control region has a length of 1581 bp which is between rrnS and trnI genes with the AT content high to 85.96%. Phylogenetic analysis indicated that Tambocerus sp. was clustered in a closely related subgroup with Homalodisca vitripennis and Empoasca vitis. This is consistent with the result of the traditional taxonomy.

Complete mitochondrial genome of Bombus terrestris (Hymenoptera: Apidae)

In this study, complete mitochondrial genome of the large earth bumblebee, Bombus terrestris, was first determined. The mitochondrial genome is 174 000 bp in length, and encodes 1 D-loop region, 2 ribosomal RNA genes, 13 protein-coding genes and 20 transfer RNA genes. Average GC content of this genome is 15%. nad6 and cob are overlapped with 12 bp, while atp8 and atp6 are overlapped with 18 bp. Phylogeny analysis indicates Bombus species exhibit closer genetic distance with Melipona species than with Apis species.

S1 gene sequence analysis of new variant isolates of avian infectious bronchitis virus in Tunisia

Purpose

Tissue samples were collected from suspected broiler flocks showing respiratory signs to identify infectious bronchitis virus (IBV), characterize emerging field strains, and study their relationships with the Massachusetts H120 strain, the only IB vaccine used in Tunisia.

Samples and methods

Several IBV isolates were identified from field samples collected from flocks located in different regions in the northeast of Tunisia. The IBV isolates were characterized and compared to commonly used vaccine strains (including 793B, D274, and H120 types), other reference IBV strains from Europe, and the recently characterized Tunisian field variants TN20/00, TN200/01, and TN335/01. Reverse transcription-polymerase chain reaction and nucleotide sequencing analyses of the hypervariable regions of the S1 gene were carried out.

Results

Four new IBV variants were isolated during the period 2007-10 and were designated TN295/07, TN296/07, TN556/07, and TN557/07. The amino acid sequence data showed 100% similarity between TN295/07 and TN296/07, suggesting that these two isolates are identical and belong to the same genotype. Similar results were demonstrated for TN556/07 and TN557/07. Sequence identity values indicated that TN296/07 and TN556/07 share 55% amino acid homologies between each other, but are very different from the reference IBV serotypes, in particular the H120 strain. It was also shown that they have 50%-77% similarities with the Tunisian virus isolated between 2000 and 2001. Phylogenetic clustering allowed classification of these Tunisian isolates as new genotypes that are closer to TN200/01, TN335/01 Tunisian field variants, and Italy02 variant than MassH120 vaccine strain.

Conclusion

S1 sequence analyses confirmed the cocirculation of H120 vaccine strain with novel IBV variants isolated from Tunisian field.