PHYLOGENETIC RELATIONSHIPS AMONG GIANT PANDA AND RELATED SPECIES BASED ON RESTRICTION SITE VARIATIONS IN rDNA SPACERS

In this study, non radioactive Digoxigenin labeled ribosomal DNA(rDNA) probes were used for Southern blotting analysis to study the molecular phylogeny of the giant panda and related species. Restriction maps in the regions of rDNA spacers were compared between giant panda( Ailuropoda melanoleuca ), lesser panda( Ailurus fulgens ), Asiatic black bear( Selenarctos thibetanus ), sun bear( Helarctos malayanus ), raccoon( Procyon lotor ) and lynx( Felis lynx ). Phylogenetic trees for these species were constructed using maximum likelihood and parsimony method. The results show that in respect to rDNA RFLPs, the giant panda is more closely related to bear than to lesser panda; while the lesser panda is slightly related to the raccoon.

Phylogenetic Relationships of Caragana(Fabaceae) by the Use of nrITS Sequences

[Objective] The aim was to explore the phylogenetic relationships of Cara- gana （Fabaceae） by the use of nrlTS sequences. [Method] Internal transcribed spac- er （ITS） sequences of nuclear ribosomal DNA （nrDNA） from 29 taxa of Caragana species and seven close relatives （all belong to Astralinae （Adens） Benth） were used for phylogenetic analysis. [Result] Length of the entire ITS region ranges from 611 to 614 bp in Caragana species. The aligned sequences nrlTS of Caragana are 655 bp, and 170 sites are variable, with 107 phylogenetically informative sites. The phylogenetically informative sites are 16.3% of the total aligned sequences. The ITS sequences data are useful to resolve some relationships at lower taxonomic levels within Caragana. The Caragana Fabr. is not a monophyletic group with very close connection with Calophaca tianschanica. The ITS data revealed that the species of Sect. tragacanthoides were dispersed in MP tree or ME tree. Although the morphol- ogy of C. ordosica is similar to C. tibetica, the ITS results revealed an unexpectedly close relativeship to C. roborovskyi. The ITS data also indicate C. davazamcii, C. korshinskii, C. intermedia, and C. microphylla are different species. [Conclusion] ITS sequences have an important reference value in exploring the relationships of Cara- gana.

PHYLOGENETIC RELATIONSHIPS OF THE ENDEMIC CHINESE CYPRINID FISH Pseudogyrinocheilus prochilus

Evidence is provided to support the hypothesis that the taxa Pseudogyrinocheilus, Semilabeo, and Discolabeo form a monophyly in which Semilabeo and Discolabeo are sister groups, and both together constitute the sister group of Pseudogyrinocheilus. On the basis of phylogenetic relationships of Pseudogyrinocheilus to others, it is proposed that the taxon Pseudogyrinocheilus be a valid genus. In addition, comments are made on importance of some features used in the traditional taxonomy of the subfamily Labeoninae.

Phylogenetic Relationships and Status Quo of Colonies for Gayal Based on Analysis of Cytochrome b Gene Partial Sequences

Thirty-three mutations and four different haplotypes were found when cytochrome b（Cytb） gene partial sequences of 12 gayals were analyzed. Together with sequences of Bos indicus, Bos taurus, Bos grunniens, and Bos gaurus with Bubalus bubalis as the out group, the partial sequences of Cytb gene of gayals were aligned and base composition and nucleotide variation of Cytb gene were analyzed. The phylogenetic trees were constructed by the NJ method and the MP method respectively, both supporting almost the same topology. Gayal is an independent species of Bos from Bos indicus, Bos taurus, and Bos gaurus. The results also indicate that a great proportion of gayal bloodline was invaded by other species, and the protection of gayal is facing a formidable situation.

The Phylogenetic Relationships among Four Subspecies of the Genus Locusta Based on Sequences of Three Subunit of Cytochrome Oxidase

[Objective] The aim was to explore the phylogenetic relationships among four subspecies of the genus Locusta.[Method] The sequences of three subunits of cytochrome oxidase of Locusta migratoria tibetensis and Locusta migratoria manilensis were amplified and sequenced（COⅠ 1 539 bp,COⅡ 684 bp,CO Ⅲ 792 bp,with the total of 3 015 bp）.The corresponding sequenses of Locusta migratoria migratoria and Locusta migratoria migratorioides were obtained from GenBank and constructed a multiple alignment.Phylogenic trees of four subspecies of L.migratoria were constructed by Neighbor-Joining,Maximum-parsimony and Bayesian,respectively.[Result] The average content of A ＋ T in three subunits of four subspecies was 69.57%;the third site of codon showed the highest A ＋ T content,and the COⅠ had the highest A ＋ T content（87.6%）;The nucleotide substitution mainly occurred at the third site of codon,and the nucleotide replacement rate of CO Ⅱ was the highest.The second site of codon was conservative,so the replacement rate was in the range of 5.9%-15%.The start codon of COⅠ was CCG or ACG.Genetic distances among four subspecies were ranged from 0.001 to 0.076.The relationship between L.m.tibetensis and Locusta migratoria manilensis was the closest,followed by L.m.migratorioides and L.m.migratorioides,while the genetic distance between L.m.tibetensis and L.m.migratorioides was the largest.[Conclusion] The phylogenetic relationships among four subspecies of Locusta migratoria is L.m.tibetensis,L.m.manilensis,L.m.migratoria,L.m.migratorioides.

A preliminary analysis of phylogenetic relationships of Arundinaria and related genera based on nucleotide sequences of nrDNA （ITS region） and cpDNA （trnL-F intergenic spacer）

Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNA trnL-F intergenic spacer (IGS). Comparison with trnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of the trnL-F IGS sequence.The tree obtained by combining both sets of data showed that the species sampled in Arundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (including A. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica and Brachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus of Arundinaria. The topologies of the trees generated from individual data and the combined data were similar.

Evaluation of the effect of genetic diversity and phylogenetic relationships on different strains of Staphylococcus aureus in clinical specimens

Introduction:Staphylococcus aureus is one of the main pathogens in humans.Also,this bacterium can be colonized in the nose.The spa gene is present in all strains of Staphylococcus aureus(S.aureus)and can be used to identify species and toxins such as Panton-Valentine Leukocidin(PVL)that can affect a wide range of skin,soft tissue,and necrotizing pneumonia.Arthritis and life-threatening infections.This study aimed to investigate the effect of genetic diversity and phylogenetic relationships on different strains of Staphylococcus aureus in clinical specimens.Methods:This review study was conducted in 2021 by searching for keywords such as genetic diversity,phylogenetics,and Staphylococcus aureus in reputable databases such as pub med and google scholar.Finally,30 articles were found,of which 30 articles were used out of 26 articles.Results:In general,23%and 18%of health care workers and patients were carriers,respectively.The incidence of methicillin-resistant Staphylococcus aureus(MRSA)is higher in the relevant population.The molecular types of MRSA isolates indicate that the most common virulence gene is Hla,and the most common type of SCCmec is SCCmec type III.Conclusion:Sites with high risk of Staphylococcus aureus should be highly protected,and relevant personnel should be paid attention and health management.

Phylogenetic Relationships in Genus Arachis Based on SSR and AFLP Markers

Fourteen wild species of different sections in the genus Arachis and 24 accessions of the AABB allotetraploid A. hypogaea （cultivated peanut） from several countries which belong to different botanical varieties, were analyzed by SSR and AFLP marker systems. The assay-units per system needed to distinguish among all the tested accessions were at least five for SSR or two for AFLP. The genetic distance detected by the SSR markers ranged from 0.09 to 0.95, and the mean was 0.73; and the genetic distance detected by the AFLP markers ranged from 0.01 to 0.79 with an average of 0.42. All the tested peanut SSR primer pairs were multilocus ones, and the amplified fragments per SSR marker in each peanut genome ranged from 2 to 15 with the mean of 4.77. The peanut cultivars were closely related to each other, and shared a large numbers of SSR and AFLP fragments. In contrast, the species in the genus Arachis shared few fragments. The results indicated that the cultivated peanut （A. hypogaea L.） varieties could be partitioned into two main groups and four subgroups at the molecular level, and that A. duranensis is one of the wild ancestors of A. hypogaea. The lowest genetic variation was detected between A. cardenasii and A. batizocoi, and the highest was detected between A. pintoi and the species in the section Arachis. The relationships among the botanical varieties in the cultivated peanut （A. hypogaea L.） and among wild species accessions in section Arachis and those in other sections in the genus Arachis were discussed.

Phylogenetic Relationships of Sorghum and Related Species Inferred from Sequence Analysis of the nrDNA ITS Region

Analysis of phylogenetic and evolution in six species of Sorghum was based on internal transcribed spacer （ITS） sequences in nuclear ribosomal DNA. Results showed that the length of the ITS regions among the six species ranged from 588 to 589 bp and the contents of G＋C in ITS （ITS1 ＋5.8S＋ITS2） regions ranged from 60.27 to 61.05%; the length of ITS1 ranged from 207 to 208 bp and the contents of G ＋ C in the ITS 1 regions ranged from 53.91 to 61.54%. The length of the 5.8S rDNA and ITS2 regions in the six species was 164 and 217 bp respectively, and the contents of G ＋ C ranged from 56.10 to 58.54% in the 5.8S rDNA region and 66.36 to 67,28% in the ITS2 region. Among regions of ITS, ITS1, ITS2, and 5.8S, the best sequence for genetic relationship analysis in the six species was the ITS region. On the basis of the Jaccard coefficient and phylogentic tree, S. sp. was more related to S, propinguum than to other species. This was consistent with the fact that S. sp. is derived from S. propinguum. From the phylogenetic tree based on ITS1, S. halepense, silk sorghum and S. sudanense, are identical in the ITS 1 sequence, whereas the phylogenetic tree based one shows that S. sudanense has a closer genetic association with S. almum rather than with S. halepense and silk sorghum.

Phylogenetic relationships among five species of Armeniaca Scop. (Rosaceae) using microsatellites (SSRs) and capillary electrophoresis

The genus Armeniaca Scop. is well known for its popular cultivated edible fruit trees such as Armeniaca vul- garis Lam. and ornamental flowers such as A. mume Sieb. Another species, A. cathayana Fu et al., one of six important dry fruits （kernel-using apricot）, is cultivated for its edible seeds in North China. In the present study, DNA from 70 individuals of A rmeniaca, including 38 of A. cathayana, 18 ofA. vulgaris, 12 ofA. sibirica, 1 ofA. dasycarpa and 1 of A. mume, was extracted and analyzed using microsatellites and capillary electrophoresis. For 20 polymorphic loci selected, 339 alleles and 140.7 effective alleles were detected. The number of alleles per locus ranged from 8 to 28, with an average of 16.95 alleles per locus. The observed heterozygosity （Ho） and the expected heterozygosity （He） ranged from 0.427 to 0.971 and from 0.737 to 0.912, respectively. The polymorphism information content varied from 0.708 to0.905, with an average of 0.827. Based on the genetic similarity among 70 individuals, a UPGMA was used to establish the phylogenetic relationships. The taxonomic positions among five species were clearly revealed, and A. cathayana was more closely related to A. vulgaris than to A. sibirica. The results will provide a scientific basis for research on the taxonomy, germplasm resources and breeding ofArmeniaca, especially for A. cathayana.

Phylogenetic analysis of 48 gene families revealing relationships between Hagfishes, Lampreys, and Gnathostomata

It has become clear that the extant vertebrates are divided into three major groups, that is, hagfishes, lampreys, and jawed vertebrates. Morphological and molecular studies, however, have resulted in conflicting views with regard to their interrelationships. To clarify the phylogenetic relationships between them, 48 orthologous protein-coding gene families were analyzed. Even as the analysis of 34 nuclear gene families supported the monophyly of cyclostomes, the analysis of 14 mitochondrial gene families suggested a closer relationship between lampreys and gnathostomes compared to hagfishes. Lampreys were sister group of gnathostomes. The results of this study supported the cyclostomes. Choice of outgroup, tree-making methods, and software may affect the phylogenetic prediction, which may have caused much debate over the subject. Development of new methods for tackling such problems is still necessary.

Phylogenetic and morphometric relationships between two species of genus Auxis from the South China Sea and Java Sea

This study was aimed at examining the phylogenetic and morphometric relationship of frigate tuna（Auxis thazard） and bullet tuna（Auxis rochei） using mt DNA D-loop（control） region sequences and truss measurements,respectively. Maximum-likelihood（ML） tree and median-joining network showed that haplotypes from Auxis populations grouped separately. Discriminant function analyses and non-metric multidimensional scaling of morphometric data showed that bullet and frigate tuna were differed mainly with respect to truss measurements on the anterior region, suggesting adaptation to different diets available in different environments. Historic demographic analyses of sequence data showed that both bullet and frigate tuna had not undergone a significant sudden population expansion recently. Non-significant value of Tajimas＇ s D and Fu＇s F_S were indicated an effective large and stable population size for longer period of both species in South China Sea and Java Sea species. This study gives first report on the complementary relationship between morphometric and genetic analysis in stock discrimination of genus Auxis.

The complete mitochondrial genome of Parachiloglanis hodgarti and its phylogenetic position within Sisoridae

The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized,which is the first mitogenome of the genus Parachiloglanis within Sisoridae.The mitogenome is 16511-bp long and included 13 protein-coding genes,22 transfer RNAs,two ribosomal RNAs,and one control region.The genome composition was A+T biased(58.64%)and exhibited a positive AT-skew(0.095)and a negative GC-skew(-0.283).Compared with other Sisoridae fishes,the characteristics of nucleotide skews,codon usage,and amino acid usage of the P.hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes.Furthermore,the phylogenetic trees show that Sisoridae fishes fall into four major clades and P.hodgarti(CladeⅠ)is basal to the Sisoridae family,forming a sister clade to the Glyptosternoids(CladeⅣ).The topological structures constructed in this study raised doubts over the traditional classification system.These results will help better understand the feature s of the P.hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.

Phylogenetic Relationship and Molecular Divergence Dating Using SRY Gene Polymorphism about Four Ladoum Sheep Lineages in Senegal

Animal genetic resources are playing a vital role in livestock production and are essential to food security. The present study aims to contribute to a better understanding genetic local sheep breeds and to elucidate the phylogenetic relationships through the evolution of the SRY gene in four different lineages of Ladoum sheep raised in Senegal. After a brief analysis of genetic diversity, the phylogenetic relationships and molecular dating were inferred through haplotype networks and four phylogenetic reconstruction methods. The different haplotype networks are constructed with NETWORK ver. 5.0.0.0 using the Median-Joining method. Phylogenetic trees were reconstructed using neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference. The robustness of the nodes in phylogenetic trees of the three first methods was assessed by 1000 bootstraps. For Bayesian inference, the posterior probability distribution of the trees was estimated by 4 MCMC chains. 5,000,000 generations were performed for each of the chains by sampling the different parameters every 1000 generations. Results show a low polymorphism. Haplotypic diversity is much higher than the average nucleotide divergence between all pairs of haplotypes. The majority and central haplotype indicates a close relationship between “Batling” and “Tyson” individuals. “Birahim” lineage is very distinct from the rest. Phylogenetic trees confirm two genetically separate clades between “Birahim” and the other lineages. The period of divergence between “Birahim” lineage versus the common ancestor of the other three lineages was 2504 years ago. The polyphyly revealed in “Birahim” lindicates that this lineage does not contain the common ancestor of all individuals who compose it. It could therefore be derived from two or more sheep breeds with a common ancestor, Ovis aries. The monophyletic clade appears to be a group including a common ancestor and all of its genetic descendants. This group, bringing together the other three lineages, is in the process of being structured into sub-lineages. This study is the first to show that there are only two genetic lines within ladoum sheep in Senegal.

Genome-Wide Identification of Tomato (Solanum lycopersicum L.) CKX Gene Family and Expression Analysis in the Callus Tissue under Zeatin Treatment

The cytokinin oxidase/dehydrogenase(CKX)enzyme is essential for controlling thefluctuating levels of endogen-ous cytokinin(CK)and has a significant impact on different aspects of plant growth and development.Nonethe-less,there is limited knowledge about CKX genes in tomato(Solanum lycopersicum L.).Here we performed genome-wide identification and analysis of nine SlCKX family members in tomatoes using bioinformatics tools.The results revealed that nine SlCKX genes were unevenly distributed onfive chromosomes(Chr.1,Chr.4,Chr.8,Chr.10,and Chr.12).The amino acid length,isoelectric points,and molecular weight of the nine SlCKX proteins ranged from 453 to 553,5.77 to 8.59,and 51.661 to 62.494 kD,respectively.Subcellular localization analysis indi-cated that SlCKX2 proteins were located in both the vacuole and cytoplasmic matrix;SlCKX3 and SlCKX5 pro-teins were located in the vacuole;and SlCKX1,4,6,7,8,and 9 proteins were located in the cytoplasmic matrix.Furthermore,we observed differences in the gene structures and phylogenetic relationships of SlCKX proteins among different members.SlCKX1-9 were positioned on two out of the three branches of the CKX phylogenetic tree in the multispecies phylogenetic tree construction,revealing their strong conservation within phylogenetic subgroups.Unique patterns of expression of CKX genes were noticed in callus cultures exposed to varying con-centrations of exogenous ZT,suggesting their roles in specific developmental and physiological functions in the regeneration system.These results may facilitate subsequent functional analysis of SlCKX genes and provide valu-able insights for establishing an efficient regeneration system for tomatoes.

Phylogenetic Relationship of an Extremely Endangered Species, Pinus squamata (Pinaceae) Inferred from Four Sequences of the Chloroplast Genome and ITS of the Nuclear Ribosomal DNA

Pinus squamata X. W. Li, a recently-described species of the Pinaceae, is an extremely endangered pine with only 32 individuals in the wild. This species was thought to be intermediate between P. bungeana Zuec. ex Endl. of subgen. Strobus and P. yunnanensis Franch. of subgen. Pinus by the original author. We made an effort to address the question of the phylogenetic relationship of this peculiar and important species in the context of the major groups of the genus Pinus by using sequences of the rbcL, matK,genes, rpl20-rps18 spacer, trnV intron of the chloroplast genome and the nuclear ribosomal ITS region. The results of the separated analysis and the combined analysis of the four cpDNA sequences and ITS sequence indicated that P. squamata was a stable member of subsect. Gerardianae and P. gerardiana Wall. was the closest species of P. squamata phylogenetically. As a result, the causes of the distribution pattern of subsect. Gerardianae were also discussed.

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

The complete mitochondrial genome （16,837 bp） from the Keeled box turtle （Pyxidea mouhotii） was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule： a large number of （ATTATATC） n direct tandem repeats followed by （TA） n microsatellite at the 3＇ end of the control region （D-loop）, which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood （ML） and Bayesian （BI） analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1） Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group （containing Pyxidea） may have originated from two ancestors; 2） the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.

Phylogenetic Analysis on SLG and SRK Genes in Brassica and Raphanus

S-locus genes were cloned from three Brassica napus and three B. campestris lines by using PCR walking and homologuesequence methods. A phylogenetic gene tree was constructed based on the six cloned genes and fifty-one previouslyreported SLG/SRK genes of Brassica and Raphanus. The SLGs from R. sativus were dispersed in the phylogenetic treeintermingling with SLG/SRKs from B. oleracea, B. napus and B. campestris. The SLG/SRK genes of classⅡclusteredindependently in one group. The SLG/SRK genes of classⅠshowed to be more divergent than classⅡgenes. Theseresults suggested that the divergence of classⅠand classⅡ should have occurred before the differentiation of thegenera Brassica and Raphanus. In addition, SLG and SRK of the same S haplotypes belonged to the same class. Itsuggested that class-Ⅰ and class-Ⅱ group divergence occurred first, and then SLG and SRK diverged. The three SC SRKgenes from B. napus and B. campestris were grouped into one cluster, displaying difference from the SC SLG of B.oleracea. These three SC SRK genes were close to SI SRK of SI1300, SI271 and guanyou in phylogenetic relationships.These results indicated that SC and SI genes diverged more recently. It is not clear yet whether the differentiation of SCand SI genes was earlier than the differentiation of Brassica and Raphanus. Studies based on more genes are necessaryfor a comprehensive elucidation of the phylogenetic relationships in Brassicaceae.

New record of the feather star Palaeocomatella hiwia(Echinodermata:Crinoidea:Comatulida)from Zhenbei Seamount in South China Sea:new insights into the taxonomic position of Palaeocomatella

One specimen belonging to the family Comatellinae was collected from the Zhenbei Seamount(332.5–478.2 m)in the South China Sea in July 2022.Based on the morphological characters,the specimen was identified as Palaeocomatella hiwia McKnight,1977.It is first recorded from China Sea and redescribed in detail.This specimen differs from the original description from New Zealand for never showing syzygy at br4+5 or br5+6 on interior and br1+2 on exterior arms.However,it is much conform to the redescription to specimens from Indonesia,with only differences in position of the second syzygy and distalmost pinnule comb.Specimen is deposited in the Institute of Oceanology,Chinese Academy of Sciences.Phylogenetic analyses based on the mitochondrial c oxidase subunit I(COI)and 16S rRNA genes indicated that P.hiwia was nested within the tribe Phanogeniini and clustered with Aphanocomaster pulcher.Furthermore,P.hiwia showed same morphological features in terms of mouth placement,comb location,and number of comb teeth rows as other genera of Phanogeniini.Therefore,we suggest that the genus Palaeocomatella should be put in the tribe Phanogeniini.

Analysis on the Origin and Phylogenetic Status of Tong Sheep Using 12 Blood Protein and Nonprotein Markers

This study is based on the Tong sheep obtained by the random sampling method of typical colonies in the central area of Baishui County in Shaanxi Province, China. An investigation was undertaken to clarify the gene constitution of blood protein and nonprotein types of Tong sheep. Twelve genetic markers were examined by starch-gel electrophoresis and cellulose acetate electrophoresis. Polymorphism in Tong sheep was found at the following 10 loci, transferrin （Tf）, alkaline phosphatase （Alp）, leucine aminopeptidase （Lap）, arylesterase （Ary-Es）, hemoglobin-β （Hb-β）, X-protein （X-p）, carbonic anhydrase （CA）, catalase （Cat）, malate dehydrogenase （MDH）, and lysine （Ly）, whereas, albumin （A1） and postalbumin （Po） loci were monomorphic. Genetic approach degree method and phylogenetic relationship clustering method were used to judge the origin and phylogenetic status of Tong sheep. Results from both methods maintained that Tong sheep belonged to the ＂Mongolia group＂, and Mongolia sheep was the origin of Tong sheep. This was also supported by the history of Tong sheep breeding. Compared to the phylogenetic relationship clustering method, the genetic approach degree method was more reliable for the extraction from East and South of Central Asia, and was more effective in reflecting the breeding course of Tong sheep.