Base Pairs In Length Research Articles

Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.

The Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo. Muscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene. The complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species.

Characterization and phylogenetic analysis of the chloroplast genome of Solanum pseudocapsicum (Solanaceae)

Solanum pseudocapsicum Linnaeus 1753, a popular indoor potted plant known for its ornamental fruits, had its chloroplast genome sequenced in this study to determine its phylogenetic relationship with other related species and to construct a phylogenetic analysis tree. The research findings are as follows: 1. The chloroplast genome of S. pseudocapsicum comprises a large single-copy (LSC) region of 86,260 base pairs, a small single-copy (SSC) region of 18,325 base pairs, and two inverted repeat (IR) regions, each measuring 25,390 base pairs in length. 2. The G + C content of the entire chloroplast genome is 37.59%, with the highest G + C content found in the IR regions, reaching 43.03%; followed by the LSC region, which has a G + C content of 35.68%; and the lowest in the SSC region, with a G + C content of 31.53%. 3. The genome contains 127 genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, with 18 genes duplicated in the IR regions. 4. Phylogenetic analysis revealed that S. pseudocapsicum, Solanum betaceum, Solanum laciniatum, and Solanum nitidum are genetically closely related and are located on the same branch of the phylogenetic tree, indicating a close relationship among them. This study provides a foundation for the identification, classification, and exploration of genetic diversity within the Solanum genus.

Transcriptome sequencing and identification of full-length genes involved in the biosynthesis of anticancer compounds Oleanolic acid and Ursolic acid in Achyranthes aspera L.

Achyranthes aspera is renowned for its rich medicinal properties since the Ayurvedic era. This plant is known for the presence of experimentally validated anticancer compounds like oleanolic acid and ursolic acid. Our study involved sequencing the RNA from the root tissue of A. aspera to elucidate the genes responsible for synthesizing these two critical secondary metabolites. Through RNA-Seq analysis, we assembled approximately 167,698 transcripts, averaging 847 base pairs in length, with an N50 value of 1509 bp. From this data, we mapped 604 sequences involved in the metabolism of terpenoids and polyketide pathways. Among them, 241 transcripts were mapped to the triterpenoid biosynthesis pathway, which included 127 transcripts involved in OA and UA biosynthesis. From these transcripts, we identified 22 full-length genes coding for all the 21 enzymes required for OA and UA biosynthesis. Identifying these full-length genes will lead to a better understanding of the pathway and adopting genetic engineering approaches.

High-throughput single telomere analysis using DNA microarray and fluorescent in situ hybridization.

The human telomere system is highly dynamic. Both short and long leucocyte average telomere lengths (aTL) are associated with an increased risk of cancer and early death, illustrating the complex relationship between TL and human health and the importance of assessing TL distributions with single TL analysis. A DNA microarray and telomere fluorescent in situ hybridization (DNA-array-FISH) approach was developed to measure the base-pair (bp) lengths of single telomeres. On average 32000 telomeres were measured per DNA sample with one microarray chip assaying 96 test DNA samples. Various telomere parameters, i.e. aTL and the frequency of short/long telomeres, were computed to delineate TL distribution. The intra-assay and inter-assay coefficient of variations of aTL ranged from 1.37% to 3.98%. The correlation coefficient (r) of aTL in repeated measurements ranged from 0.91 to 1.00, demonstrating high measurement precision. aTLs measured by DNA-array-FISH predicted aTLs measured by terminal restriction fragment (TRF) analysis with r ranging 0.87-0.99. A new accurate and high-throughput method has been developed to measure the bp lengths of single telomeres. The large number of single TL data provides an opportunity for an in-depth analysis of telomere dynamics and the complex relationship between telomere and age-related diseases.

Solvation free energy in governing equations for DNA hybridization, protein-ligand binding, and protein folding.

This work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the equilibria. In the first example, the binding affinities of two DNA duplexes, one of nine and one of 10 base pairs in length, are measured and characterized by isothermal titration calorimetry (ITC) as a function of concentration. The results indicate that the change in solvation free energy that accompanies duplex formation (ΔGS) is large and unfavorable. The duplex with the larger number of G:C pairings yields the largest change in solvation free energy, ΔGS = +460 kcal·mol-1per base pair at 25 °C. A van't Hoff analysis of the data is complicated by the varying degree of intramolecular base stacking within each DNA strand as a function of temperature. A modeling study reveals how the solvation free energy alters the output of a typical ITC experiment and leads to a good, though misleading, fit to the classical equilibrium equation. The same thermodynamic framework is applied to a model protein-ligand interaction, the binding of ribonuclease A with the nucleotide inhibitor 3'-UMP, and to a conformational equilibrium, the change in tertiary structure of α-lactalbumin in molar guanidinium chloride solutions. The ribonuclease study yields a value of ΔGS = +160 kcal·mol-1, whereas the folding equilibrium yields ΔGS ≈ 0, an apparent characteristic of hydrophobic interactions. These examples provide insight on the role of solvation energy in binding equilibria and suggest a pivot in the fundamental application of thermodynamics to solution chemistry.

Complete mitochondrial genome sequence of the white root rot pathogen Dematophora necatrix (Xylariaceae: Xylariales)

The mitochondrial genome of Dematophora necatrix is 121,350 base pairs in length with a G + C content of 30.19%. Phylogenetic analysis showed that D. necatrix grouped with other members of the Xylariaceae, with which its mitogenome also shares a broadly similar architecture and gene content. The D. necatrix mitogenome contains 14 protein-coding and 26 tRNA-encoding genes, as well as one copy each of the rnl, rns, rps3 and nat1 genes. However, as much as 80% of this genome is intronic or non-coding. This is likely due to expansions and rearrangements caused by the large number of group I introns and the homing endonucleases and reverse-transcriptases they encode. Our study thus provides a valuable foundation from which to explore the mitochondrion’s role in the biology of D. necatrix, and also serves as a resource for investigating the pathogen’s population biology and general ecology.

Identification and antibacterial activity of a novel phage-type lysozyme from the freshwater mussel Hyriopsis cumingii

A cDNA encoding a phage-type lysozyme, designated as HcPLYZ, was successfully cloned from Hyriopsis cumingii. The full-length cDNA sequence of HcPLYZ was determined to be 896 base pairs in length. Analysis revealed the absence of a signal peptide at its N-terminus, and identified two highly conserved phage-type lysozyme activity sites, Glu20 and Asp29, within the deduced amino acid sequence of HcPLYZ. The results of the cloning and sequencing symbiotic bacteria in tissues were consistent with those obtained using tissue cDNA as the template, suggesting that HcPLYZ may originate a symbiotic bacterium. The expression levels of HcPLYZ mRNA exhibited significant variations across different tissues. Successful expression was induced using IPTG, and the native recombinant protein was subsequently purified through affinity chromatography employing Ni2+, and the optimal pH and temperature of which were determined to be 5.5 and 50°C, respectively. Following exposure to Aeromonas hydrophila, there was a significant increase in the levels of HcPLYZ mRNA in the hemocytes, hepatopancreas, and gills. HcPLYZ was demonstrated the inhibition activity of 55% and 83% against Micrococcus lysodeikticus under pH 5.5 and 50 °C conditions, respectively. These results suggested that HcPLYZ possessed antibacterial activity against both A. hydrophila and M. lysodeikticus.

Characteristics and functional analysis of a novel mannose receptor in Penaeus vannamei

The mannose receptor (MR) plays a key role in the innate immune system as a pattern recognition receptor. Here, a novel type of mannose receptor, named PvMR2, was identified from Penaeus vannamei (P. vannamei). The PvMR2 coding sequence (CDS) obtained was 988 base pairs in length, encoding a protein consisting of 328 amino acids. This protein includes a signal peptide and two classical C-type lectin domains (CTLD). Quantitative real-time PCR showed that PvMR2 was distributed in all detected tissues, with the highest levels in the intestines and stomach. Following a bacterial challenge with Vibrio anguillarum (V. anguillarum), PvMR2 showed significant up-regulation in both the intestines and stomach of shrimp. To validate the function of PvMR2, recombinant proteins were extracted and purified using a His-tag. The resulting rPvMR2 demonstrated binding capability with lipopolysaccharides (LPS) and peptidoglycan (PGN) in a dose-dependent manner, affirming its binding affinity. The purified rPvMR2 demonstrated calcium-independent binding activity towards both Gram-positive bacteria (V. anguilliarum and Vibrio parahaemolyticus) and Gram-negative bacteria (Escherichia coli and Aeromonas Veronii). Antibacterial assays confirmed that rPvMR2 inhibits bacterial growth. Intestinal adhesion and adhesion inhibition experiments confirmed that the rPvMR2 can be used to reduce the adhesion capacity of harmful bacteria in the gut. Phagocytosis experiments have shown that rPvMR2 promotes phagocytosis in hemocytes and protects the host from external infection. Treatment with recombinant PvMR2 significantly bolstered bacterial clearance within the hemolymph and markedly augmented shrimp survival post-infection with V. anguillarum. These results suggest that PvMR2 has agglutination, growth inhibition, adhesion inhibition, clearance promotion, and phagocytosis effects on harmful bacteria, and plays a crucial role in the antimicrobial immune response of P. vannamei.

Broad-range amplification and sequencing of the rpoB gene: a novel assay for bacterial identification in clinical microbiology.

The rpoB gene has been proposed as a promising phylogenetic marker for bacterial identification, providing theoretically improved species-level resolution compared to the 16S rRNA gene for a range of clinically important taxa. However, its utility in diagnostic microbiology has been limited by the lack of broad-range primers allowing for its amplification from most species with a single PCR assay. Here, we present an assay for broad-range partial amplification and Sanger sequencing of the rpoB gene. To reduce cross-reactivity and allow for rpoB amplification directly from patient samples, primers were based on the dual priming oligonucleotide principle. The resulting amplicon is ~550 base pairs in length and appropriate for species-level identification. Systematic in silico evaluation of a wide selection of taxa demonstrated improved resolution within multiple important genera, including Enterococcus, Fusobacterium, Mycobacterium, Streptococcus, and Staphylococcus species and several genera within the Enterobacteriaceae family. Broad-range rpoB amplification and Sanger sequencing of 115 bacterial isolates provided unambiguous species-level identification for 97 (84%) isolates, as compared to 57 (50%) using a clinical 16S rRNA gene assay. Several unresolved taxonomic matters disguised by the low resolution of the 16S rRNA gene were revealed using the rpoB gene. Using a collection of 33 clinical specimens harboring bacteria and assumed to contain high concentrations of human DNA, the rpoB assay identified the pathogen in 29 specimens (88%). Broad-range rpoB amplification and sequencing provides a promising tool for bacterial identification, improving discrimination between closely related species and making it amenable for use in culture-based and culture-independent diagnostic approaches.

Assembly and Annotation of the Complete Genome Sequence of the Paenibacillus Bacteriophage phJNUCC32

A potential biocontrol agent for American foulbrood (AFB), the Paenibacillus bacteriophage phJNUCC32, was isolated from Baengnokdam in Halla Mountain. This study aimed to investigate its genomic characteristics through whole-genome sequencing. The genome of phJNUCC32 was found to be 62,871 base pairs in length, with a G + C content of 51.98%. Phylogenetic analysis classified phJNUCC32 within the unclassified Caudoviricetes bacteriophage category. The genome prediction confirmed the absence of virulence factors and antibiotic-resistance genes, ensuring its genetic safety. A total of 63 coding DNA sequences were identified, revealing a modular arrangement. Notably, the annotation of gene function indicates that phJNUCC32 harbors the holin/lysin system, suggesting significant potential for controlling bacterial infections in AFB and agriculture.

The Complete Chloroplast Genome of Syzygium syzygioides (Myrtaceae: Myrtales) and Phylogenetic Analysis

Abstract Background: Syzygium syzygioides (Miq.) Merr. and L. M. Perry is a common medicinal plant species known for its biologically active compounds. However, the chloroplast (cp) genome of S. syzygioides has not been previously reported. This study aimed to determine the complete cp genome sequence of S. syzygioides and investigate its phylogenetic relationships within the Syzygium genus. Methods: Leaf samples of S. syzygioides were collected from Vietnam, and the complete cp genome was sequenced and assembled. Phylogenetic analyses were then conducted to examine the evolutionary relationships between S. syzygioides and other Syzygium species. Results: The cp genome of S. syzygioides was found to be 158,172 base pairs in length, with a GC content of 37.0%. Phylogenetic reconstruction based on the cp genome data revealed that S. syzygioides is closely related to 10 other Syzygium species, including Syzygium buettnerianum, Syzygium bamagense, Syzygium grande, Syzygium megacarpum, Syzygium glomeratum, Syzygium claviflorum, Syzygium tsoongii, Syzygium fluviatile, Syzygium buxifolium, and Syzygium grijsii. Conclusions: This study provides the first report of the complete cp genome sequence of S. syzygioides, a medicinally important plant species in the Myrtaceae family. The phylogenetic analysis using the cp genome data sheds light on the evolutionary relationships within the Syzygium genus, which is the largest genus in the Myrtaceae. The new molecular data generated in this study can be used for the molecular identification and further phylogenetic investigations of Syzygium species, contributing to a better understanding of the diversity and evolutionary history of this economically and ecologically significant plant group.

Identification and functional characterization of galectin-3 in silver pomfret (Pampus argenteus)

Galectin-3, as a unique member of the galectin family, exhibits a significant role in both extracellular and intracellular environments. In this study, the silver pomfret galectin-3 gene (SpGal-3) was cloned and functionally characterized. The open reading frame of SpGal-3 was found to be 843 base pairs in length, encoding a protein of 280 amino acids. Phylogenetic tree analysis indicated that SpGal-3 was highly conserved in fish species. The mRNA of SpGal-3 was expressed at various levels in all tested tissues, with the gill exhibiting the highest expression levels. Furthermore, infection with Photobacterium damselae subsp. damselae significantly changed the mRNA expression of SpGal-3 in liver and head kidney tissues. Subcellular localization analysis suggested that SpGal-3 was expressed in both the nucleus and cytoplasm. Purified recombinant protein of SpGal-3, designated as rSpGal-3, showed binding ability to two classic pathogen-associated molecular patterns (peptidoglycan and lipopolysaccharide) and two sugars (D-mannose and D-galactose), with the highest affinity toward lipopolysaccharide. Additionally, rSpGal-3 demonstrated the capability to interact with various bacterial species. Taken together, our findings underscore the critical role of SpGal-3 as a key pattern recognition receptor in the immune response of the silver pomfret.

Levels of 5α-reductase gene in intestinal lavage fluid decrease with progression of colorectal cancer.

Introduction. Colorectal cancer (CRC) is a leading cause of cancer deaths, closely linked to the intestinal microbiota and bile acid metabolism. Secondary bile acids, like deoxycholic and lithocholic acid, are associated with increased CRC risk due to their disruption of vital cellular functions. In contrast, isoallolithocholic acid (isoalloLCA) shows potential health benefits, highlighting the complex role of bile acids in CRC. A specific primer set was previously developed to amplify homologs of the 5α-reductase gene (5ar), which are involved in the biosynthesis of isoalloLCA, thereby enabling the estimation of abundance of 5ar (5ar levels) in the intestine.Hypothesis/Gap Statement. We hypothesized that 5ar levels in the intestine are associated with CRC.Aim. This study aimed to investigate intestinal 5ar levels and compare them across different stages of the adenoma-carcinoma sequence, providing insights into novel strategies for monitoring CRC risk.Methodology. DNA was extracted from intestinal lavage fluids (ILF) collected during 144 colonoscopies. Next-generation sequencing (NGS) was employed to examine the sequence of 5ar homologues, using a specific primer set on DNA from seven selected ILFs - four from carcinoma patients and three from individuals with non-neoplastic mucosa. Additionally, we used quantitative PCR (qPCR) to measure 5ar levels in all 144 DNA samples.Results. We conducted 144 colonoscopies and categorized patients according to the adenoma-cancer sequence: 52 with non-neoplastic mucosa, 69 with adenomas and 23 with carcinoma. Analysis of 292,042 NGS-derived 5ar sequences revealed the seven most prevalent amplicon sequence variants, each 254 base pairs in length. These closely matched or were identical to 5ar sequences in Bacteroides uniformis, Phocaeicola vulgatus and Phocaeicola dorei. Furthermore, qPCR analysis demonstrated significantly lower 5ar levels in the carcinoma group compared to those in the non-neoplastic mucosa group (P = 0.0004). A similar, though not statistically significant, trend was observed in the adenoma group (P = 0.0763), suggesting that 5ar levels decrease as CRC progresses.Conclusion. These findings indicate that PCR-based monitoring of 5ar levels in intestinal samples over time could provide a non-invasive, rapid and cost-effective method for assessing an increased risk of CRC.

The complete chloroplast genome sequence of Ampelopsis delavayana Planchon. ex Franch 1886 (Vitaceae)

Ampelopsis delavayana Planchon. ex Franch 1886 is a plant with significant pharmacological effects and ornamental importance. This research unveiled the complete chloroplast (cp) genome sequence of A. delavayana. The study highlights that the cp genome of A. delavayana possesses a distinct tetrameric structure spanning 162,497 base pairs, comprising a small single-copy (SSC) region of 18,902 base pairs, a large single-copy (LSC) region of 90,441 base pairs, and two inverted-repeat regions (IRs), each 26,577 base pairs in length. The GC content of the SSC, LSC, and IR regions of the genome was 31.80%, 35.16%, and 42.82%, respectively, culminating in an overall GC content of 37.27%. The genome comprised 130 genes, which included eight rRNAs, 36 tRNAs, and 86 protein-coding genes. Through phylogenetic analysis utilizing the maximum-likelihood method, it was established that A. delavayana was closely related to Ampelopsis glandulosa var. brevipedunculata, positioning it as a sister species. This report not only provides a scientific reference for understanding the phylogeny of the family Vitaceae but also enriches our genetic information of Ampelopsis.

Clinical, pathological, and molecular features of central nervous system tumors with BCOR internal tandem duplication

Central nervous system tumor with BCOR internal tandem duplication (CNS tumor with BCOR-ITD) constitutes a molecularly distinct entity, characterized by internal tandem duplication within exon 15 of the BCOR transcriptional co-repressor gene (BCOR-ITD). The current study aimed to elucidate the clinical, pathological, and molecular attributes of CNS tumors with BCOR-ITD and explore their putative cellular origin. This study cohort comprised four pediatric cases, aged 23 months to 13 years at initial presentation. Magnetic resonance imaging revealed large, well-circumscribed intra-CNS masses localized heterogeneously throughout the CNS. Microscopically, tumors were composed of spindle to ovoid cells, exhibiting perivascular pseudorosettes and palisading necrosis, but lacking microvascular proliferation. Immunohistochemical staining showed diffuse tumor cell expression of BCOR, CD56, CD99, vimentin, and the stem cell markers PAX6, SOX2, CD133 and Nestin, alongside focal positivity for Olig-2, S100, SOX10, Syn and NeuN. Molecularly, all cases harbored BCOR-ITDs ranging from 87 to 119 base pairs in length, including one case with two distinct ITDs. Notably, the ITDs were interrupted by unique 1–3 bp insertions in all cases. In summary, CNS tumors with BCOR-ITD exhibit characteristic clinical, pathological, and molecular features detectable through BCOR immunohistochemistry and confirmatory molecular analyses. Their expression of stem cell markers raises the possibility of an origin from neuroepithelial stem cells rather than representing true embryonal neoplasms.

Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements.

The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.

CAREx: context-aware read extension of paired-end sequencing data

BackgroundCommonly used next generation sequencing machines typically produce large amounts of short reads of a few hundred base-pairs in length. However, many downstream applications would generally benefit from longer reads.ResultsWe present CAREx—an algorithm for the generation of pseudo-long reads from paired-end short-read Illumina data based on the concept of repeatedly computing multiple-sequence-alignments to extend a read until its partner is found. Our performance evaluation on both simulated data and real data shows that CAREx is able to connect significantly more read pairs (up to 99%\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$99\\%$$\\end{document} for simulated data) and to produce more error-free pseudo-long reads than previous approaches. When used prior to assembly it can achieve superior de novo assembly results. Furthermore, the GPU-accelerated version of CAREx exhibits the fastest execution times among all tested tools.ConclusionCAREx is a new MSA-based algorithm and software for producing pseudo-long reads from paired-end short read data. It outperforms other state-of-the-art programs in terms of (i) percentage of connected read pairs, (ii) reduction of error rates of filled gaps, (iii) runtime, and (iv) downstream analysis using de novo assembly. CAREx is open-source software written in C++ (CPU version) and in CUDA/C++ (GPU version). It is licensed under GPLv3 and can be downloaded at (https://github.com/fkallen/CAREx).

Mitogenomic profiling of Marcia recens (Holten, 1802): a step towards taxonomic resolution of India's Ashtamudi short-neck clam

ABSTRACT The Ashtamudi short-neck clam forms a significant fishery resource holding India’s first Marine Stewardship Council Certification. The taxonomic classification of this particular clam has engendered debate regarding its proper nomenclature. The present study aims to provide its first comprehensive mitogenome profile from the type locality to address the existing taxonomic ambiguity. The mitogenome assembled using the genome skimming method had 17,991 base-pair length with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and control region. Phylogenetic analysis based on the concatenated data set of PCGs and rRNAs from 47 representative species of Veneridae grouped all species including short-neck clams from the subfamily Tapetinae into a single clade. This analysis also revealed the polyphyly of the genus Marcia. Nevertheless, the short-neck clam co-clustered with Marcia recens from Chinese waters. Subsequent mitochondrial gene order, genetic distance and morphological analyses substantiated the closer relationship of this clam to the genus Marcia, analogous to the phylogenetic output. The genomic data from the type locality provides additional molecular and phylogenetic evidence for the classification of short-neck clam in the genus Marcia. This will also help to address long-standing taxonomic uncertainties surrounding this species, offering valuable information critical for management and conservation of the resource.

Influence of breed and environment on leukocyte telomere length in cattle.

High milk yield is associated with reduced longevity in high-producing dairy cattle breeds. Pre-term culling leads to high replacement heifer demand and economic losses for the dairy industry. Selection for this trait is limited because of low heritability and difficulties in phenotype measurement. Telomeres are elements found at the ends of chromosomes, consisting of repetitive DNA sequences, several thousand base pairs in length, coupled with nucleoprotein complexes. Eventually, in humans and most other animals, telomere length reduces with age. When telomeric DNA is truncated to a critical length, cell ageing, cell cycle arrest, and apoptosis are induced. As a result, telomere length can be considered as a predictor of health risks and an individual's lifespan. The leukocyte telomere length may be used as a proxy phenotype of productive lifespan to improve cattle selection. Our objectives were to assess the effects of breed and breed group (dairy vs. beef) on the leukocyte telomere length and to estimate the effect of cold climate on this trait in Kalmyk cattle populations from the South (Rostov Oblast) and Far North (Republic of Sakha) regions of Russia. The leukocyte telomere lengths were estimated computationally from whole-genome resequencing data. We leveraged data on leukocyte telomere length, sex, and age of 239 animals from 17 cattle breeds. The breed factor had a significant effect on leukocyte telomere length across our sample. There was no difference in leukocyte telomere length between dairy and beef groups. The population factor had a significant effect on leukocyte telomere length in Kalmyk animals. In conclusion, we found that breed, but not breed group (dairy vs. beef), was significantly associated with leukocyte telomere length in cattle. Residence in colder climates was associated with longer leukocyte telomere length in Kalmyk breed cattle.

Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China

A new species of inquiline gall wasp, Synergus nanlingensis Wang & Zeng, sp. nov., which was reared from galls on Castanopsis eyrei Tutch (Fagaceae) collected in Guangdong Province, China, is described and illustrated herein along with its mitochondrial genome. The mitogenome of S. nanlingensis is 16,604 base pairs in length and comprises 37 genes, which is typical of mitogenomes. One large control region was detected in the S. nanlingensis mitogenome, which differed from that reported for other Cynipidae species. Similar to other Cynipidae species, S. nanlingensis has the same four common gene rearrangement events; however, it shows some differences, as follows: trnS1 is downstream of Cytb; trnS2 is upstream of nad1; and trnC is downstream of rrnS. Phylogenetic analysis using COI, CytB, and 28S-D2 sequences confirmed that S. nanlingensis is a distinct species belonging to the genus Synergus Hartig.