Bp In Length Research Articles

Identification and Functional Characterization of the SaMYB113 Gene in Solanum aculeatissimum.

The MYB transcription factors (TFs) have substantial functions in anthocyanin synthesis as well as being widely associated with plant responses to various adversities. In the present investigation, we found an unreported MYB TF from Solanum aculeatissimum (a wild relative of eggplant) and named it SaMYB113 in reference to its homologous gene. Bioinformatics analysis demonstrated that the open reading frame of SaMYB113 was 825 bp in length, encoding 275 amino acids, with a typical R2R3-MYB gene structure, and predicted subcellular localization in the nucleus. Analysis of the tissue-specific expression pattern through qRT-PCR showed that the SaMYB113 was expressed at a high level in young stems as well as leaves of S. aculeatissimum. Transgenic Arabidopsis and tobacco plants overexpressing SaMYB113 pertinent to the control of the 35S promoter exhibited a distinct purple color trait, suggesting a significant change in their anthocyanin content. Furthermore, we obtained three tobacco transgenic lines with significant differences in anthocyanin accumulation and analyzed the differences in anthocyanin content by LC-MS/MS. The findings demonstrated that overexpression of SaMYB113 caused tobacco to have considerably raised levels of several anthocyanin components, with the most significant increases in delphinidin-like anthocyanins and cyanidin-like anthocyanins. The qRT-PCR findings revealed significant differences in the expression levels of structural genes for anthocyanin synthesis among various transgenic lines. In summary, this study demonstrated that the SaMYB113 gene has a substantial impact on anthocyanin synthesis, and overexpression of the SaMYB113 gene leads to significant modifications to the expression levels of a variety of anthocyanin-synthesizing genes, which leads to complex changes in anthocyanin content and affects plant phenotypes. This present research offers the molecular foundation for the research of the mechanism of anthocyanin formation within plants, as well as providing some reference for the improvement of traits in solanum crops.

Identification and characterization of two Bacillus anthracis bacteriophages

Anthrax is an acute infectious zoonotic disease caused by Bacillus anthracis, a bacterium that is considered a potential biological warfare agent. Bacillus bacteriophages shape the composition and evolution of bacterial communities in nature and therefore have important roles in the ecosystem community. B. anthracis phages are not only used in etiological diagnostics but also have promising prospects in clinical therapeutics or for disinfection in anthrax outbreaks. In this study, two temperate B. anthracis phages, vB_BanS_A16R1 (A16R1) and vB_BanS_A16R4 (A16R4), were isolated and showed siphovirus-like morphological characteristics. Genome sequencing showed that the genomes of phages A16R1 and A16R4 are 36,569 bp and 40,059 bp in length, respectively. A16R1 belongs to the genus Wbetavirus, while A16R4 belongs to the genus Hubeivirus and is the first phage of that genus found to lyse B. anthracis. Because these two phages can comparatively specifically lyse B. anthracis, they could be used as alternative diagnostic tools for identification of B. anthracis infections.

CHARACTERIZATION OF THE CHLOROPLAST GENOME OF AQUILARIA CRASSNA PIERRE EX LECOMTE DISTRIBUTED IN VIETNAM USING LONG-READ DATA (OXFORD NANOPORE TECHNOLOGIES)

Aquilaria crassna Pierre ex Lecomte is a critically endangered species that is famous for its fragrance compounds for perfume and incense production. In this study, the complete chloroplast genome of A. crassna was sequenced using a long-read sequencing method of Oxford Nanopore Technologies. The complete chloroplast genome of A. crassna was 174,766 bp in length, which comprised a large single copy region of 87,231 bp, a small single copy region of 3,343 bp, and two inverted repeat regions of 42,096 bp. This genome contained 95 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. The analysis ofsmall single repeats revealed 39 mononucleotide and seven dinucleotide repeats, which are located mainly in non-coding regions. Comparative genomic analysis exhibited high conservation of the chloroplast genome within the Aquilaria genus regarding gene content, gene order, and genomic structure. This study provides useful genomic data for further studies examining the genetic population, genetic conservation, molecular markers, and phylogeny of Aquilaria crassna and related species within Thymelaeaceae.

Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata

BackgroundThe disputed phylogenetic position of Aerides flabellata Rolfe ex Downie, due to morphological overlaps with related species, was investigated based on evidence of complete chloroplast (cp) genomes. The structural characterization of complete cp genomes of A. flabellata and A. rosea Lodd. ex Lindl. & Paxton were analyzed and compared with those of six related species in “Vanda-Aerides alliance” to provide genomic information on taxonomy and phylogeny.ResultsThe cp genomes of A. flabellata and A. rosea exhibited conserved quadripartite structures, 148,145 bp and 147,925 bp in length, with similar GC content (36.7 ~ 36.8%). Gene annotations revealed 110 single-copy genes, 18 duplicated in inverted regions, and ten with introns. Comparative analysis across related species confirmed stable sequence identity and higher variation in single-copy regions. However, there are notable differences in the IR regions between two Aerides Lour. species and the other six related species. The phylogenetic analysis based on CDS from complete cp genomes indicated that Aerides species except A. flabellata formed a monophyletic clade nested in the subtribe Aeridinae, being a sister group to Renanthera Lour., consistent with previous studies. Meanwhile, a separate clade consisted of A. flabellata and six Vanda R. Br. species was formed, as a sister taxon to Holcoglossum Schltr.ConclusionsThis research was the first report on the complete cp genomes of A. flabellata. The results provided insights into understanding of plastome evolution and phylogenetic relationships of Aerides. The phylogenetic analysis based on complete cp genomes showed that A. flabellata should be placed in Vanda rather than in Aerides.

The complete chloroplast genomes of Polygonatum hunanense, P. verticillatum, and P. caulialatum and their phylogenetic positions

Polygonatum hunanense H.H. Liu & B.Z. Wang (2021) and P. verticillatum (L.) All. (1875) have been widely used as foods and as folk medicines in China and India, and P. caulialatum S. R. Yi (2021) has recently been described as a new medical plant in China. There is at present a lack of genome information regarding the species. Hence, this study reports the complete chloroplast genomes of the three species. The genomes of P. hunanense, P. verticillatum, and P. caulialatum were 155,583 bp, 155,650 bp, and 155,352 bp in length, respectively. They contained large single-copy (LSC) regions of 84,412 bp, 84,404 bp, and 84,285 bp, small single-copy (SSC) regions of 18,427 bp, 18,416 bp, and 18,463 bp, and a pair of inverted repeats of 26,372 bp, 26,415 bp, and 26,302 bp, respectively. The chloroplast genomes of P. hunanense, P. verticillatum, and P. caulialatum had 133 (103 unique) genes, consisting of 87 protein-coding genes, 38 ribosomal ribonucleic acid (RNA) genes, and eight transfer RNA genes, respectively. A maximum-likelihood phylogenetic tree showed that P. kingianum Coll. et Hemsl. var. grandifolium D.M. Liu & W.Z. Zeng (1991) was closer to P. cyrtonema Hua (1892) rather than to P. kingianum Coll. et Hemsl. (1890), further supporting its status as a unique species of the genus. Moreover, P. verticillatum was separated from the easily confused herb P. cirrhifolium (Wall.) Royle (1839), while P. caulialatum was closest to P. humile Fisch. ex Maxim. (1859). This research provides a foundation for further study of these herbs.

Genomic Sequencing and Analysis of Enzootic Nasal Tumor Virus Type 2 Provides Evidence for Recombination within the Prevalent Chinese Strains.

In recent years, the clinical cases of ENTV-2 infection have increased and become prevalent in several provinces of China. In this study, we reported the occurrence of ENTV-2 in one goat farm in Chongqing, southwest China. The complete genome of an emerged ENTV-2 isolate (designated as CQ2) was sequenced with 7468 bp in length. Phylogenetic analysis revealed that ENTV-2 consisted of two main lineages. Lineage 1 was composed of Chinese strains and could be subdivided into five sublineages. CQ2 and the other six recent isolates from China were clustered in sublineage 1.5; however, CQ2 was significantly different from the other six isolates. Furthermore, recombination analysis suggested that CQ2 might be a recombinant variant derived from sublineage 1.5 and sublineage 1.2 strains, with the recombination region in areas of pro and pol genes. In conclusion, we sequenced and analyzed the complete genome of a potential ENTV-2 recombinant, which may contribute to our understanding of the genetic variation and evolution of ENTV-2 in China.

The complete chloroplast genome of Meconopsis torquata (Papaveraceae), a traditional Tibetan medicine

Meconopsis torquata Prain 1906, a national second-class rare and endangered plant, is reported here for the first time for its complete chloroplast genome. The genome is 153,290 bp in length, comprising a large single-copy region (LSC, 83,918 bp), a small single-copy region (SSC, 17,740 bp), and two inverted repeat sequences (IRa and IRb, each 25,816 bp). The overall GC content is 38.7%, with the IR region having the highest content (43.1%). The genome is annotated with 112 unique genes, including 4 rRNA genes, 29 tRNA genes, and 79 protein-coding genes. Analysis of codon usage bias reveals that codons ending in A/T account for 96.7% of those with a Relative Synonymous Codon Usage (RSCU) value above 1. This predominance of A/T-ending codons might be indicative of M. torquata adaptation to high-altitude environments. Phylogenetic analysis reveals a close kinship between M. torquata and M. pinnatifolia and M. paniculata, indicating that the ancestral groups of these species might have a complex evolutionary history. This study uncovers the genetic characteristics and adaptive evolution of M. torquata, offering a new perspective in understanding the phylogenetic relationships within the genus. The findings not only provide a solid theoretical foundation for the conservation and sustainable use of this rare and endangered species but also offer significant scientific support for the conservation of biodiversity.

The complete chloroplast genome of the first registered Paeonia Itoh hybrid cv. Hexie in China

The first registered Paeonia Itoh hybrid cv. Hexie in China is a naturally occurring intersectional hybrid of Sect. Paeonia and Sect. Moutan. In this study, we sequenced, assembled, and analyzed the complete chloroplast genome of Paeonia Itoh hybrid cv. Hexie. The result showed that the chloroplast genome of Hexie, with a typical circular tetrad structure, is 152,958 bp in length, comprising a large single copy (LSC) region of 84,613 bp, a small single copy (SSC) region of 17,051 bp, and two reverse complementary sequences (IRs) of 25,647 bp. The chloroplast genome encoded 116 genes, including 80 protein-coding genes, 32 tRNA genes, and 4 rRNA genes. Phylogenetic analysis inferred from the shared protein-coding genes showed that the Paeonia Itoh hybrid cv. Hexie had the closest phylogenetic relationship with P. suffruticosa, followed by P. ostii, indicating that P. suffruticosa was its maternal parent. This study provides a molecular resource for phylogenetic and maternal parent studies of Paeonia Itoh hybrid, contributing to a basis for Paeonia Itoh hybrid breeding strategies in the future.

The complete chloroplast genome sequence of Olea dioica Roxb, 1820 (Oleaceae)

Olea dioica Roxb, 1820 is a very important ethnomedicinal tree because of its medicinal properties and it belongs to the Oleaceae family. It is mainly distributed in evergreen and semi-evergreen forests. However, the chloroplast genome of O. dioica has not yet been reported. In this study, the chloroplast genome sequence of O. dioica was sequenced using next-generation sequencing technologies. The complete chloroplast genome of O. dioica was 155,138 bp in length (GenBank accession no. PP048999), comprising a large single-copy (LSC) region of 86,048 bp, a small single-copy (SSC) region of 17,816 bp, and two inverted repeat (IR) regions 25,637 bp each. The overall GC content was 37.8%. The complete chloroplast genome of O. dioica contains 131 complete genes, which are 88 protein-coding genes, 35 transfer RNA genes, and eight ribosomal RNA genes. A maximum-likelihood (ML) tree of O. dioica and 14 other species in the family Oleaceae suggested that O. dioica showed a close relationship with Olea brachiata.

Phylogenetic analysis of Cyprinus acutidorsalis (Wang, 1979) from the Hainan population using complete mitochondrial genome

Cyprinus acutidorsalis (Wang, 1979) is an endemic fish in China that is sparsely distributed in the Hainan provinces and Guangxi Zhuang Autonomous Region (GZAR). In this study, the complete mitochondrial genome of C. acutidorsalis from the Hainan population from the Wanquan River was sequenced, and its phylogenetic relationship was analyzed. The circular mtDNA was 16,581 bp in length, and the overall base composition was A (32.0%), C (27.5%), T (24.8%), and G (15.70%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis indicated that the most closely related fish to C. acutidorsalis from the Hainan population was C. acutidorsalis from the Guangxi population. These findings offer basic molecular data and a better understanding of the phylogenetic relationships among the Cyprinus species.

New mitogenomes of Runcinidae and Facelinidae: two understudied heterobranch families (Mollusca: Gastropoda)

Here, we present the mitochondrial sequences of two sea slugs (Heterobranchia): Runcina aurata and Facelina auriculata, the latter being the type species of the family. The mitochondrial genomes are 14,282 and 14,171bp in length, respectively, with a complete set of 13 PCGs, 2 rRNAs, and 22 tRNAs. None of the mitogenomes show gene reorganization, keeping the standard mitogenomic structure of Heterobranchia. Nucleotide composition differs significantly between them, with R. aurata showing the most AT-rich mitogenome (25.7% GC content) reported to date in Heterobranchia, and F. auriculata showing a rich GC content (35%) compared with other heterobranch mitochondrial genomes.

The complete mitochondrial genome of Anidiocerus bimaculatus Zhang, Li & Qi, 2008 (Hemiptera: Cicadellidae: Eurymelinae: Idiocerini)

In this study, the complete mitochondrial genome of Anidiocerus bimaculatus was sequenced and annotated for the first time, which belongs to the subfamily Eurymelinae. The mitogenome of A. bimaculatus was 15,267 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding control region. In this mitogenome, all the PCGs are initially encoded by ATT, ATA, ATG, or TTG, and terminated by TAA, or single T. The overall base composition of A. bimaculatus is 43.6% adenines, 36.0% thymines, 9.1% guanines, and 11.3% cytosines. ML phylogenetic analyses confirmed that Idiocerini forms a monophyletic clade and the newly sequenced A. bimaculatus clustered within the Idiocerini clade based on 13 protein-coding genes and two rRNA genes.

Complete mitochondrial genome of the worm snail Thylacodes adamsii (Littorinimorpha: Vermetidae) from South Korea

The worm snail Thylacodes adamsii (Mörch, 1859) (Littorinimorpha: Vermetidae) is a sessile gastropod that mainly inhabits rocky shores along the warm temperate to tropical ocean. Herein, the complete mitochondrial genome (mitogenome) of T. adamsii from South Korea was characterized. The genome is 14,913 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The genome organization and base composition of T. adamsii are similar to those of other vermetids. A phylogenetic tree was reconstructed using maximum likelihood based on the nucleotide sequences of the 13 PCGs; this tree supported the monophyly of Vermetidae. The complete mitogenome of T. adamsii can assist with molecular species identification and vermetid phylogenetic research in the future.

The complete mitochondrial genome of a ground beetle Synuchus nitidus (Carabidae: Harpalinae: Sphodrini) from South Korea

The ground beetle Synuchus nitidus (Motschulsky, 1861) (Carabidae: Harpalinae: Sphodrini) is one of the most common species in the forests of South Korea, which has the potential to be utilized as an environmental indicator. Here, we characterized the complete mitochondrial genome (mitogenome) of S. nitidus, which is the first in the harpaline tribe Sphodrini. Its genome is 16,392 bp in length and composed of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A + T rich region. In addition, we reconstructed a maximum likelihood tree to elucidate the phylogenetic position of Sphodrini among the seven harpaline tribes using nucleotide sequences of the 13 PCGs. The ML tree supported a monophyletic clade of the subfamily Harpalinae and showed a close relationship between Sphodrini and Lebinii with a low bootstrap value. The complete mitogenome of S. nitidus could be helpful for molecular species identification and exploring phylogenetic relationships among carabids.

The complete mitochondrial genome of bamboo shrimp Atyopsis moluccensis (Atyidae, Decapoda)

Atyopsis moluccensis, belonging to the family Atyidae, is one of the popular species in aquarium industry. Here, we sequenced the mitochondrial genome of A. moluccensis. The mitogenome of A. moluccensis is 15,933 bp in length, consisting 22 transfer RNAs, 13 protein-coding genes (PCGs), and two ribosomal RNAs. The composition of A. moluccensis mitogenome is 33.77% for A, 13.81% for G, 28.74% for T, and 23.68% for C. The A + T content of the heavy-strand was 62.51%. Except ND5, most of the PCGs had ATN as the start codon. Only COX2 and ND4 were stopped by incomplete stop codon. The phylogenetic relationship was reconstructed with 16 shrimp from six genera of family Atyidae, which revealed that A. moluccensis and A. gabonensis clustered together and species of the same genus were grouped together in a clade. The data are beneficial in understanding the evolution and phylogenetic relationships of Atyidae shrimp.

The complete mitochondrial genome of Zaomma eriococci (hymenoptera: encyrtidae)

The complete mitochondrial genome of the Zaomma eriococci (Ferrière, 1955) (Hymenoptera: Encyrtidae) was obtained through next-generation sequencing, making the first reported complete mitochondrial genome of the genus Zaomma. The mitochondrial genome is 15,648 bp in length and includes 37 classical eukaryotic mitochondrial genes along with an A + T rich region. All 13 protein-coding genes (PCGs) initiate with typical ATN codons. Of these, 10 PCG genes terminate with TAA, while three terminate with TAG. Additionally, there are 22 tRNA genes, ranging in size from 62 to 70 bp. The maximum likelihood phylogenetic tree was constructed based on 13 PCGs, indicates that Z. eriococci is closely related to Tassonia gloriae. This mitochondrial genome will serve as a valuable molecular resource for species identification, genetic analysis, and comparative genomic studies of Z. eriococci, contributing to the growing collection of mitochondrial genomes within the family Encyrtidae.

Characterization of the complete chloroplast genome sequence of Bassia scoparia (L.) A. J. Scott 1978 (Amaranthaceae) and its phylogenetic analysis

Bassia scoparia, an annual potherb belonging to the family Amaranthaceae, has been widely used in traditional Chinese and Japanese medicine for over 2000 years. Herein, we presented its complete chloroplast. The chloroplast genome sequence was 151,278 bp in length with a 36.6% content of GC. The genome showed the typical quadripartite structure, comprising a pair of inverted repeat (IR) regions (24,353 bp) separated by a large single-copy (LSC) region (84,067 bp) and a small single-copy (SSC) region (18,505 bp). This chloroplast genome harbored 133 predicted genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that B. scoparia was closely related to B. littorea. This newly sequenced chloroplast genome not only enhances our understanding of the genome of Bassia but also provides valuable insights for the evolutionary study of the family Amaranthaceae.

Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae)

Oreomecon nudicaulis, commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis, which was previously classified under the genus Papaver, was reclassified within the genus Oreomecon. Nevertheless, the phylogenetic status and chloroplast genome within the genus Oreomecon have not yet been reported. This study elucidates the chloroplast genome sequence and structural features of O. nudicaulis and explores its evolutionary relationships within Papaveraceae. Using Illumina sequencing technology, the chloroplast genome of O. nudicaulis was sequenced, assembled, and annotated. The results indicate that the chloroplast genome of O. nudicaulis exhibits a typical circular quadripartite structure. The chloroplast genome is 153,903 bp in length, with a GC content of 38.87%, containing 84 protein-coding genes, 8 rRNA genes, 38 tRNA genes, and 2 pseudogenes. The genome encodes 25,815 codons, with leucine (Leu) being the most abundant codon, and the most frequently used codon is AUU. Additionally, 129 microsatellite markers were identified, with mononucleotide repeats being the most abundant (53.49%). Our phylogenetic analysis revealed that O. nudicaulis has a relatively close relationship with the genus Meconopsis within the Papaveraceae family. The phylogenetic analysis supported the taxonomic status of O. nudicaulis, as it did not form a clade with other Papaver species, consistent with the revised taxonomy of Papaveraceae. This is the first report of a phylogenomic study of the complete chloroplast genome in the genus Oreomecon, which is a significant genus worldwide. This analysis of the O. nudicaulis chloroplast genome provides a theoretical basis for research on genetic diversity, molecular marker development, and species identification, enriching genetic information and supporting the evolutionary relationships among Papaveraceae.

CRISPR-Cas9 mediated genome editing of Kluyveromyces marxianus for iterative, multiplexed gene disruption and pathway integration.

Kluyveromyces marxianus, a thermotolerant, fast-growing, Crabtree-negative yeast, is a promising chassis for the manufacture of various bioproducts. Although several genome editing tools are available for this yeast, these tools still require refinement to enable more convenient and efficient genetic modification. In this study, we engineered the K. marxianus NBRC 104275 strain by impairing the nonhomologous end joining and enhancing the homologous recombination machinery, which resulted in improved homology-directed repair effective on homology arms of up to 40 bp in length. Additionally, we simplified the CRISPR-Cas9 editing system by constructing a strain for integrative expression of Cas9 nuclease and plasmids bearing different selection markers for gRNA expression, thereby facilitating iterative genome editing without the need for plasmid curing. We demonstrated that tRNA was more effective than the hammerhead ribozyme for processing gRNA primary transcripts, and readily assembled tRNA-gRNA arrays were used for multiplexed editing of at least four targets. This editing tool was further employed for simultaneous scarless in vivo assembly of a 12-kb cassette from three fragments and marker-free integration for expressing a fusion variant of fatty acid synthase, as well as the integration of genes for starch hydrolysis. Together, the genome editing tool developed in this study makes K. marxianus more amenable to genetic modification and will facilitate more extensive engineering of this nonconventional yeast for chemical production.

A Full-Length Transcriptome and Analysis of the NHL-1 Gene Family in Neocaridina denticulata sinensis.

Neocaridina denticulata sinensis has emerged as a promising model organism for basic studies in Decapod. However, the current transcriptome information on this species is based on next-generation sequencing technologies, which are limited by a short read length. Therefore, the present study aimed to generate a full-length transcriptome assembly of N. denticulata sinensis utilizing the PacBio Sequel Ⅱ platform. The resulting transcriptome assembly comprised 5831 transcripts with an N50 value of 3697 bp. Remarkably, 90.5% of these transcripts represented novel isoforms of known genes. The transcripts were further searched against the NR, SwissProt, KEGG, KOG, GO, NT, and Pfam databases. A total of 24.8% of the transcripts can be annotated across all seven databases. Additionally, 1236 alternative splicing events, 344 transcription factors, and 124 long non-coding RNAs (LncRNAs) were predicted. Based on the alternative splicing annotation results, a RING finger protein NHL-1 gene from N. denticulata sinensis (NdNHL-1) was identified. There are 15 transcripts in NdNHL-1. The longest transcript is 4995 bp in length and encodes a putative protein of 1665 amino acids. A phylogenetic analysis showed its close relationship with NHL-1 from other crustacean species. This report represents the full-length transcriptome of N. denticulata sinensis and will facilitate research on functional genomics and environmental adaptation in this species.