Multi-gene phylogeny of Jattaea bruguierae,a novel asexual morph from Bruguiera cylindrica

During our survey on marine-based ascomycetes of southern Thailand,fallen mangrove twigs were collected from the intertidal zones.Those specimens yielded a novel asexual morph of Jattaea(Calosphaeriaceae,Calosphaeriales),Jattaea bruguierae,which is confirmed as a new species by morphological characteristics such as nature and measurements of conidia and conidiophores,as well as a multigene analysis based on combined LSU,SSU,ITS andβ-tubulin sequence data.Jattaea species are abundantly found from wood in terrestrial environments,while the asexual morphs are mostly reported from axenic cultures.Jattaea bruguierae is the first documentation of an asexual morph species from marine-habitats.

Morphogenesis and Molecular Phylogeny of a Marine Urostylid Ciliate Apokeronopsis wrighti(Protista, Ciliophora, Hypotrichia)

Hypotrichs are one of the highly differentiated ciliated lineages which play important roles in ecological, environmental,evolutionary and basic biological studies. In the present study, we investigated the living characteristics, infraciliature, nuclear apparatus, ontogenesis and phylogenetic position of a marine hypotrichous ciliate, Apokeronopsis wrighti Long et al., 2008, which was isolated from coastal waters in Shenzhen, China. The new isolate resembles the type population in terms of morphological characteristics, morphometrics, and SSU rRNA gene sequence that is with a 99.7% similarity. Ontogenesis of A. wrighti is characterized by oral primordium for the proter as well as marginal and dorsal kineties anlagen in both filial products formed de novo, and the cirral row arranged along the paroral and endoral arises from several anterior frontoventral-transverse cirral streaks. Phylogenetic analyses based on SSU and concatenated gene data suggest that five species of Apokeronopsis form a monophyletic clade, and the genus Apokeronopsis is closely related to Thigmokeronopsis and Metaurostylopsis.

Mitochondrial genomes of Tapes dorsatus and Cardita variegata:insights into Heteroconchia phylogeny

Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.

Multi-gene-based investigation on the molecular phylogeny of the hypotrichous family Strongylidiidae(Protista,Ciliophora),with notes on the ontogeny of a new genus and new species

Ciliates in the subclass Hypotrichia have long been difficult to classify as they are one of the most polymorphic and highly differentiated groups,leading to their systematics remaining unresolved.Phylogenetic relationships within the hypotrich family Strongylidiidae have been ambiguous due to discordance between the morphological and genetic data.In this study,a new strongylidiid genus Heterouroleptus is established,mainly based on the novel mode of origin of the ventral cirral rows:left ventral cirral row(LVR)originates from frontal-ventral-transverse cirral anlagen(FVTA)Ⅲ(anterior portion),IV(middle portion),and V(rear portion);right ventral cirral row comes from the entire FVTA VI.A new species,Hetero-uroleptus weishanensis gen.nov.,sp.nov.,is investigated along with the morphometric and molecular data from a population of Strongylidium wuhanense.Eight new sequences and nuclear gene markers(single-gene and multi-gene)are provided to analyze the phylogenetic relationships of strongylidiids,with the COI gene utilized to uncover further genetic information at species level and below.The results reveal that:(1)Strongylidiidae is monophyletic and has a close relationship with Dorsomarginalia;(2)Heterouroleptus gen.nov.forms a clade that is sister to all the other strongylidiids;(3)Hemiamphisiella Foissner,1988 and Pseudouroleptus Hemberger,1985 should not be synonyms,and both genera should be subdivided due to their variable morphological characteristics;(4)LVR originating from three anlagen is a plesiomorphy of Strongylidiidae.The discovery of the origin of the LVR not only contributes to the establishment of the genus Heterouroleptus,but also helps to improve the diagnosis of the family Strongylidiidae.

A predictive equation for residual strength using a hybrid of subset selection of maximum dissimilarity method with Pareto optimal multi-gene genetic programming

More accurate and reliable estimation of residual strength friction angle(/r)of clay is crucial in many geotechnical engineering applications,including riverbank stability analysis,design,and assessment of earthen dam slope stabilities.However,a general predictive equation for/r,with applicability in a wide range of effective parameters,remains an important research gap.The goal of this study is to develop a more accurate equation for/r using the Pareto Optimal Multi-gene Genetic Programming(POMGGP)approach by evaluating a comprehensive dataset of 290 experiments compiled from published literature databases worldwide.A new framework for integrated equation derivation proposed that hybridizes the Subset Selection of Maximum Dissimilarity Method(SSMD)with Multi-gene Genetic Programming(MGP)and Pareto-optimality(PO)to find an accurate equation for/r with wide range applicability.The final predictive equation resulted from POMGGP modeling was assessed in comparison with some previously published machine learning-based equations using statistical error analysis criteria,Taylor diagram,revised discrepancy ratio(RDR),and scatter plots.Base on the results,the POMGGP has the lowest uncertainty with U95=2.25,when compared with Artificial Neural Network(ANN)(U95=2.3),Bayesian Regularization Neural Network(BRNN)(U95=2.94),Levenberg-Marquardt Neural Network(LMNN)(U95=3.3),and Differential Evolution Neural Network(DENN)(U95=2.37).The more reliable results in estimation of/r derived by POMGGP with reliability 59.3%,and resiliency 60%in comparison with ANN(reliability=30.23%,resiliency=28.33%),BRNN(reliability=10.47%,resiliency=10.39%),LMNN(reliability=19.77%,resiliency=20.29%)and DENN(reliability=27.91%,resiliency=24.19%).Besides the simplicity and ease of application of the new POMGGP equation to a broad range of conditions,using the uncertainty,reliability,and resilience analysis confirmed that the derived equation for/r significantly outperformed other existing machine learning methods,including the ANN,BRNN,LMNN,and DENN equations。

Improved mammalian family phylogeny using gap-rare multiple sequence alignment:A timetree of extant placentals and marsupials

The timing of mammalian diversification in relation to the Cretaceous-Paleogene(KPg)mass extinction continues to be a subject of substantial debate.Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples.In the present study,we improved an existing dataset from the landmark study of Meredith et al.(2011)by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers.Using these two datasets,we then constructed phylogenies for extant mammalian families,providing improved resolution of many conflicting relationships.Moreover,the timetrees generated,which were calibrated using appropriate molecular clock models and multiple fossil records,indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period.Additionally,intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary,supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification.Thus,our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.

Multi-gene genetic programming extension of AASHTO M-E for design oflow-volume concrete pavements

The American Association of State Highway and Transportation Officials Mechanistic-Empirical Pavement DesignGuide (AASHTO M-E) offers an opportunity to design more economical and sustainable high-volume rigid pavementscompared to conventional design guidelines. It is achieved through optimizing pavement structural andthickness design under specified climate and traffic conditions using advanced M-E principles, thereby minimizingeconomic costs and environmental impact. However, the implementation of AASHTO M-E design for low-volumeconcrete pavements using AASHTOWare Pavement ME Design (Pavement ME) software is often overly conservative.This is because Pavement ME specifies the minimum design thickness of concrete slab as 152.4 mm (6 in.). Thispaper introduces a novel extension of the AASHTO M-E framework for the design of low-volume joint plain concretepavements (JPCPs) without modification of Pavement ME. It utilizes multi-gene genetic programming (MGGP)-based computational models to obtain rapid solutions for JPCP damage accumulation and long-term performanceanalyses. The developed MGGP models simulate the fatigue damage and differential energy accumulations. Thispermits the prediction of transverse cracking and joint faulting for a wide range of design input parameters and axlespectrum. The developed MGGP-based models match Pavement ME-predicted cracking and faulting for rigidpavements with conventional concrete slab thicknesses and enable rational extrapolation of performance predictionfor thinner JPCPs. This paper demonstrates how the developed computational model enables sustainable lowvolumepavement design using optimized ME solutions for Pittsburgh, PA, conditions.

Phylogeny,character evolution,and classification of Selaginellaceae(lycophytes)

Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions(74%increase of the earlier largest sampling)representing ca.300 species to infer a new phylogeny.The evolution of 10 morphological characters is studied in the new phylogenetic context.Our major results include:(1)the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades;(2)the Sinensis group is resolved as sister to S.subg.Pulviniella with strong support in two of the three analyses;(3)most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family;and(4)an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l.is split into seven subfamilies(corresponding to the current six subgenera t the Sinensis group)and 19 genera(the major diagnosable clades)with nine new species-poor genera.We support the conservation of Selaginella with a new type,S.flabellata,to minimize nomenclatural instability.We provide a key to subfamilies and genera,images illustrating their morphology,their morphological and geographical synopses,a list of constituent species,and necessary new combinations.This new classification will hopefully facilitate communication,promote further studies,and help conservation.

Antibiogram, Genomic and Phylogeny of Stool and Seafood Isolates from Some Cholera-Prone Coastal Communities in Rivers State, Nigeria

Cholera is a significant public health threat across the globe, especially in coastal regions with poor water supply. This study was carried out to determine the antibiogram, genomic, and phylogeny of stool and seafood isolates from some cholera-prone coastal communities in Rivers State, Nigeria. A total of 400 stool samples and 42 different seafood were aseptically collected and examined using standard microbiology and molecular techniques. An antibiogram of isolates from seafood and stool samples was assayed. Genes for virulence, resistance, and relatedness of bacteria identified were also determined. The isolates from the stool and seafood were examined for susceptibility to some selected antibiotics. The findings showed the prevalence rate of cholera in the communities as follows: 16% in Kaa, 30% in Andoni, 4% in Ogu/Bolo, and 10% in Abua/Odual. The isolates from stool were susceptible to Ciprofloxacin and Gentamycin with a susceptibility rate of 94.12% each while 100% resistance was recorded against Amoxicillin-clavulanic acid, 94.12% against Amikacin and 88.24% against Colistin. For the sea foods, the isolates were susceptible to gentamycin and ciprofloxacin with a susceptibility rate of 91.43% and 82.86% respectively. Resistance was also recorded against Colistin (88.57%) and Azithromycin (82.86%). Testing the isolates for the presence of 16SrRNA genes showed that all were positive with 1500 bp 16SrRNA gene band size. TEM, OXA, SHV, and CTX-M resistant genes were detected whereas the virulence genes were TDH and AcrB. The phylogenetic analysis revealed isolates from seafood to be Aeromonas dhakensis, Vibrio parahaemolyticus, Vibrio azureus, and Providencia rettgeri, while in stool samples they were Enterobacter sichuanensis, Enterobacter hormaechei, Providencia sneebia, and Proteus vulgaris. Providencia stuartii, Proteus mirabilis, Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae were common isolates from both seafood and stool samples. This study has shown that not all reported cases of cholera are caused by Vibrio cholerae. Therefore, attention should be paid to other water-borne bacteria in every outbreak, especially in coastal communities.

Phylogeny and Geographical Derivation of Genus Hildenbrandia Based on Morphological and Molecular Evidence

The marine and freshwater Hildenbrandia samples were collected from diverse locations of China and Japan,and mor-phological characterization and molecular phylogenetic analysis were conducted on these samples.Morphological measurements of freshwater specimens were consistent with the results of H.jigongshanensis,whereas cell dimensions of marine specimens were slightly larger than those of widely distributed H.rubra and H.crouanii.Phylogenetic trees based on rbcL,psbA and UPA sequences were consistent.Freshwater specimens collected in this study formed an independent clade with H.jigongshanensis supported by high values.Species attribution was confirmed further by the similar ITS2 secondary structures among the samples of H.jigongshan-ensis.It was found that the intraspecific divergence of rbcL gene in H.jigongshanensis was smaller than other two freshwater species H.rivularis and H.angolensis.Phylogenetic trees showed that marine specimens in this study grouped together with H.rubra samples of North America,and were different with the H.rubra samples of Europe.Combining the comparison results of CBC numbers in ITS2 secondary structure,we propose the marine samples collected in this study to be a new species Hildenbrandia qingdaoensis sp.nov.The separation of the marine and freshwater specimens was supported by the rbcL,UPA and psbA phylogeny as well as ITS2 se-condary structure inference.Biogeographical reconstruction showed the ancestor of freshwater Hildenbrandia might derive from South America and dispersed from North America to Europe and then to Asian countries,which needs to be verified further with more sam-ples and molecular evidences from South America.

石仙桃与细叶石仙桃叶绿体基因组解析及其系统发育

石仙桃和细叶石仙桃均为珍稀濒危的附生兰,两者叶绿体基因组特征及其系统发育报道较少,本研究旨在揭示石仙桃和细叶石仙桃叶绿体基因组特征及其系统发育。2022年5月取驯化栽培的石仙桃和细叶石仙桃幼嫩叶片,基于Illumina测序平台分别获得石仙桃和细叶石仙桃叶绿体序列,用GetOrganelle组装、CPGAVAS2注释,利用生物信息学方法开展重复序列、密码子偏好性、四分体边界等叶绿体特征分析,并从NCBI上下载相关的序列开展基因组比较与系统发育分析。石仙桃叶绿体基因组大小为159122 bp(GC含量为37.41%),细叶石仙桃叶绿体基因组大小为158798 bp(GC含量为37.47%),两者均包括大单拷贝区(LSC)、小单拷贝区(SSC)和反向重复序列(IRa/IRb)。石仙桃与细叶石仙桃均注释了113个基因,其中编码蛋白质的基因79个,石仙桃中编码79个蛋白质基因使用22968个密码子,编码亮氨酸的UUA相对同义密码子使用频次(RSCU)达到1.90;细叶石仙桃中编码79个蛋白质的基因使用22923个密码子,编码亮氨酸UUA的RSCU达到1.91。石仙桃叶绿体基因组中共有44个简单序列重复(SSR)、47个散在重复、26个串联重复;细叶石仙桃有32个SSR、25个散在重复、30个串联重复。石仙桃属6个物种的四分体边界及共线性无大片段变化,但存在核苷酸多态性,trn K-UUU、trn Q-UUG、rpl16等基因可作为物种的分子标记候选基因。系统分析明确了石仙桃和细叶石仙桃等石仙桃属物种与蜂腰兰和流苏贝母亲缘关系较近,并同处于附生兰的分支中,叶绿体基因组大片段倒置等可能是兰科适应生活习性改变的原因之一。本研究明确了石仙桃和细叶石仙桃叶绿体基因组特征,探讨了其系统发育及兰科生活习性与叶绿体基因组之间的关系,为进一步分类和分子标记开发等相关研究奠定了基础。

蒙古扁桃叶绿体遗传特征分析

以古老孑遗植物蒙古扁桃为试材,基于Illumina HiSeq X^(Ten)平台测序,采用生物信息学分析方法,研究了蒙古扁桃叶绿体基因组特征和系统发育情况,以期为蒙古扁桃和近缘种物种鉴定、系统发育地位以及早春观赏植物和西北荒漠草地植物的育种培育提供参考依据。结果表明:蒙古扁桃叶绿体基因组为四分体式结构。其蛋白编码基因共编码26428个密码子,有29种是偏好密码子。密码子UUU数目最多,达1034个;密码子GCG数目最少,为137个。编码亮氨酸的密码子数目最多(2637个),占总量的9.98%;编码色氨酸的密码子数目最少(531个)仅占到1.94%。根据设置参数,发现蒙古扁桃叶绿体基因组中串联重复有16个,SSR位点有31个。SSR大多位于基因间区IGS和LSC区域。SSR中未检测到三核苷酸重复。基于叶绿体全基因组序列数据发现蒙古扁桃与桃亚属的桃和甘肃桃亲缘关系较近。

无籽刺梨及其近缘种叶绿体基因组序列比较分析

【目的】探讨无籽刺梨及其近缘种之间的系统发育关系,为蔷薇属植物后期分子鉴定和群体遗传研究奠定基础。【方法】从NCBI数据库下载了6种植物的叶绿体基因组序列,包括无籽刺梨和其近缘种。利用生物信息学方法对这些基因组序列进行了研究,包括基因组结构、重复序列、高变区序列以及基于叶绿体全基因组序列的系统发育关系。【结果】6种植物的叶绿体基因组呈环状四分体结构,其长度为156561~156749 bp,平均GC含量均为37.2%,且6种植物基因组的反向重复(inverted repeat,IR)区未表现出明显的扩张和收缩。在对蔷薇属植物叶绿体基因组序列进行比较分析时,筛选出了7个高变区序列,包括trnK-trnQ、psbM-trnY、ycf3-rps4、rps4-trnL、psbE-petG、rpl16 intron和ycf1。这些序列可作为候选标记,用于进一步研究蔷薇属植物的系统发育。同时,利用叶绿体全基因组序列重建了蔷薇属植物的系统发育树。结果表明,无籽刺梨和刺梨是独立的2个种类,其中无籽刺梨与贵州缫丝花有较近的亲缘关系,而刺梨与单瓣缫丝花有较近的亲缘关系。【结论】无籽刺梨及其近缘种之间叶绿体基因组结构高度相似,单拷贝区核苷酸多样性高于重复区。

重瓣榆叶梅全叶绿体基因组遗传特征分析

【目的】对重瓣榆叶梅Prunus triloba‘Multiplex’全叶绿体基因组序列进行测序,探究其系统发育位置并分析其叶绿体基因组成特点。【方法】以重瓣榆叶梅叶片为材料,采用2×CTAB法提取叶绿体DNA,利用Illumina NovaSeq平台进行叶绿体基因组的测序,组装、注释并分析其叶绿体基因组遗传特征。联合美国国家生物技术信息中心(NCBI)数据库数据,基于全叶绿体基因组序列构建了重瓣榆叶梅系统进化关系。【结果】重瓣榆叶梅叶绿体基因组全长为157827 bp,NCBI登录号MT937181,其结构为经典的四分体结构,由1个大单拷贝区域(LSC),1个小单拷贝区域(SSC)及反向重复区域(IRa/IRb)构成,其序列长度分别为86032、19023、26386 bp。GC和AT的总占比分别为36.80%和63.20%。重瓣榆叶梅的完整叶绿体基因组序列注释到132个基因,包括tRNA基因、编码蛋白基因、rRNA基因,分别为37、87、8个。重瓣榆叶梅叶绿体基因组共编码26678个密码子和236个符合条件的SSR位点。SSR位点中A/T碱基占优势,碱基偏好性十分明显。【结论】系统进化树分析表明,重瓣榆叶梅和榆叶梅P.triloba聚合成一分支结构,与同属植物长柄扁桃P.pedunculata亲缘关系较近。

雅鲁藏布江下游鮡科鱼类分类整理及三新种和中国一新记录种

基于形态学和分子系统学方法,对1974、2019—2023年间采自雅鲁藏布江下游(我国实际控制区内,下同)的403尾鮡科鱼类标本进行分类整理。标本检视结果及结合历史记录表明,雅鲁藏布江下游共分布有鮡科鱼类6属10种,即黑斑原鮡Glyptosternon maculatum(Regan 1905)、穴形纹胸鮡Glyptothorax cavia(Hamilton1822)、墨脱纹胸鮡G.medogensis Chen&He sp.nov.、疑似细体纹胸鮡G.cf.gracilis(Günther 1864)、稀有纹胸鮡G.rara Chen&He sp.nov.、西仁褶鮡Pseudecheneis sirenica Vishwanath&Darshan 2007、扁头异鮡Creteuchiloglanis kamengensis(Jayaram 1966)、细尾鰋Exostoma tenuicaudatum Tamang,Sinha&Gurumayun2015、西藏鰋E.tibetanum Gong,Lin,Liu&Liu 2018和无斑平唇鮡Parachiloglanis immaculata Chen&He sp.nov.。新种墨脱纹胸鮡是安氏纹胸鮡G.annandalei Hora 1923种名的修订,其偶鳍具羽状皮褶,项背骨前突与上枕骨棘相离,腹鳍起点位于背鳍基后缘垂直下方之后,腹鳍末端远离臀鳍起点,更细的尾柄,以及更长的头长等联合特征区别于同属其他物种。新种稀有纹胸鮡其偶鳍腹面光滑,无羽状皮褶;胸部吸着器心形,皮纹向前延伸至咽部,附着器后缘中部微陷、开放,皮纹不明显;臀鳍不分枝鳍条11根;项背骨前突与上枕骨棘间隔距离远;上颌须延伸超过胸鳍基末端,达胸鳍长的1/2处,其长为头长的134.2%等特征区别于同属其他种。新种无斑平唇鮡是霍氏平唇鮡P.hodgarti(Hora 1923)种名修订,其上颌齿带两侧向后延伸,内侧内凹,呈弯月形,横向宽约为纵向深的2倍;下颌齿带前缘和后缘中部微凹,左右两块紧靠,无明显间隔;鳃孔下角限于胸鳍基前1/3处;脂鳍末端游离,与尾鳍起点有一缺刻;胸鳍分枝鳍条16—17根;尾鳍末端明显内凹;侧线明显,侧线孔周围具白色稀疏圆点,体表和各鳍无明显的斑纹等特征有别于同属其他物种。穴形纹胸鮡为我国新记录种。西仁褶鮡为黄斑褶鮡P.sulcata(McClelland 1842)种名的修订。文章对10种鮡科鱼类的主要鉴别特征进行了描述,并编制了属种分类检索表。

火炬花叶绿体基因组特征及系统发育

火炬花(Kniphofia uvaria(L.)Oken)为阿福花科(Asphodelaceae)火把莲属药用植物。通过组装火炬花完整的叶绿体基因组,并对其结构特征与系统发育进行分析。结果表明:火炬花叶绿体基因组全长163227 bp,为典型的四分体结构,其由一个长84414 bp的大单拷贝(LSC)和一个长17871 bp的小单拷贝(SSC)组成,由一对长30471 bp的反向重复序列(IRs)将大单拷贝区与小单拷贝区分开。火炬花基因组包含130个基因,其中蛋白质编码基因、tRNA基因、rRNA基因数量分别为84、38、8个。共鉴定简单序列重复位点75个,且以单碱基重复A、T类型为主。火炬花叶绿体基因组的58个编码序列中共有24841个密码子参与翻译蛋白表达,编码20种氨基酸,其中,亮氨酸是基因组中占比最高的氨基酸。火炬花叶绿体基因组中相对同义密码子使用率(RSCU)大于1的28种密码子均以A或U结尾。依据叶绿体基因组的系统发育分析结构可以看出,火炬花与阿福花科的14种植物亲缘关系更加密切。

三角鲤线粒体基因组全序列测定及分析

[目的]三角鲤(Cyprinus multitaeniata)是我国具有重要经济价值的鱼类之一,了解三角鲤线粒体基因的结构和特点,为三角鲤的种群遗传多样性研究提供基础资料。[方法]采用26对引物扩增三角鲤的线粒体全基因,通过生物软件识别和分析各基因和非编码序列的位置和特点,并通过与GeneBank数据库已发表鲤科鱼类序列进行比较和构建系统发育树进行分析。[结果]三角鲤线粒体全基因总长度为16 573 bp,碱基含量A为32.2%、T为24.9%、C为27.3%、G为15.6%;包括37个编码基因(编码蛋白基因13个、tRNA基因22个和rRNA基因2个)和2个非编码序列区(OL区和控制区)。13个蛋白编码基因中,COX1的起始密码子为GTG,其他均为ATG;终止密码子包括TAG(ATP8)、TA(COX3、ATP6)、T(ND2、COX2、ND3、ND4、Cty b)和TAA(ND1、COX1、ND4L、ND5、ND6)3种。22个tRNA基因中,除了tRNASer(AGC)外其余都能折叠成典型的三叶草结构;三角鲤控制区序列可以识别出3个典型保守区域;系统发育分析表明,三角鲤与大眼鲤(C.megalophthalmus)亲缘关系较近。[结论]三角鲤线粒体基因组成、长度和排列顺序与典型的脊椎动物相同,在亲缘关系上与大眼鲤最近;线粒体基因组序列适用于三角鲤的系统发育分析。

榆叶梅叶绿体基因组特征分析

【目的】对榆叶梅(Amygdalus triloba)叶绿体基因组进行特征分析,并依据基因组序列数据构建系统发育树。【方法】通过Illumina HiSeq X Ten平台对榆叶梅叶绿体基因组进行序列测序、组装和基因注释,用生物信息学分析方法对其叶绿体基因组进行特征解析。【结果】研究发现榆叶梅叶绿体基因组大小和结构与经典被子植物相似。其蛋白编码基因共编码24 930个密码子,有29个偏好密码子。其中,亮氨酸密码子数目最多,占总量的10.56%。根据设置参数,发现榆叶梅叶绿体基因组中串联重复有15个。SSR(简单重复序列)大多位于基因间区IGS和LSC区域,位点有32个。【结论】榆叶梅与同亚属长柄扁桃(Amygdalus pedunculata)和李属(Prunus)毛樱桃(Prunus tomentosa)亲缘关系较近,但与同亚属的扁桃(Amygdalus dulcis)亲缘关系较远。

2种楠属植物叶绿体基因组特征及系统发育

应用Illumina Novaseq 6000高通量测序平台进行测序,组装了完整的崖楠(Phoebe yaiensis)和红毛山楠(Phoebe hungmoensis)叶绿体基因组,并对其基因组特征、基因构成、序列重复、边界收缩、密码子偏好性及系统发育进行分析。结果表明:崖楠和红毛山楠叶绿体基因组呈现典型的四分结构,总长度分别为154144和152671 bp,2种植物叶绿体基因组注释了包含83个编码蛋白、36个tRNA和8个rRNA在内的共127条基因,均检测到118个SSR位点。密码子偏好性分析显示,均有31个高频密码子,且都偏好以A/T结尾;与近缘种叶绿体基因组对比分析发现2种植物叶绿体基因组序列都高度保守;楠属植物叶绿体基因的Ka/Ks值基本小于1,rpl16基因在所有楠属基因组相互对比组合中为正选择,可能与楠属植物对环境的适应性有关。系统发育关系显示,楠属分为3个聚类组,崖楠与粗柄楠、白楠聚为一类;红毛山楠与粉叶楠、大果楠聚为一类;竹叶楠与楠属亲缘关系比润楠属更近。

唐古特扁桃叶绿体基因组特征分析

采用Illumina HiSeq X Ten平台测序和生物信息法对唐古特扁桃叶绿体基因组序列特征进行解析。结果表明:唐古特扁桃叶绿体基因组为四分体式结构,完整叶绿体基因组序列全长158166 bp,G+C含量36.8%,注释131个基因,即86个蛋白编码基因、8个rRNA基因和37个tRNA基因;其叶绿体基因组共有52711个编码密码子,有33种类型是偏好密码子;唐古特扁桃叶绿体基因组中SSR位点有33个,串联重复有13个;SSR中未检测到三核苷酸重复;SSR分布不平衡,大多位于基因间区IGS和LSC区域;基于叶绿体全基因组序列构建系统发育建树,发现唐古特扁桃与同亚属的榆叶梅、野樱桃以及李属毛樱桃亲缘关系较近。