The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines.However,few studies have investigated intraspecies mitogenomic variati...The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines.However,few studies have investigated intraspecies mitogenomic variation.In this study,69 mitogenomes of the Black-throated Tit(Aegithalos concinnus)were assembled and annotated from a large number of short reads generated using high-throughput sequencing technology.Comparative analyses revealed that mitogenomic characteristics such as length,gene and nucleotide composition,codon usage,and duplicated control regions were relatively conserved despite substantial intraspecies morphological changes.Yet,all the individuals from the subspecies A.c.iredalei had one more nucleotide in the 12S rRNA than the other studied subspecies.Phylogenetic analyses showed five distinct lineages based on the complete mitogenomes and the 13 combined protein-coding genes,whereas only four lineages were observed when using the duplicate control regions.Most interestingly,each lineage had both copies of the control regions of the comprising individuals,indicating that the paralogous control regions were more similar than the orthologous sequences from the distinct lineages.This suggested the control regions had undergone concerted evolution.The Black-throated Tit has complex evolutionary history and needs further investigating the taxonomic status of these lineages,as well as the underlying evolutionary processes.Our findings call for more research on intraspecies mitogenomic variation.展开更多
Combined Single-Crystal XRD,solution 13C and ^(195)Pt NMR,solid-state ^(195)Pt NMR and UV-vis measurements,together with comprehensive(TD)DFT calculations,are used to describe the supramolecular interactions and seque...Combined Single-Crystal XRD,solution 13C and ^(195)Pt NMR,solid-state ^(195)Pt NMR and UV-vis measurements,together with comprehensive(TD)DFT calculations,are used to describe the supramolecular interactions and sequential concerted structural transformation occurring in a{PPh4^(+);[Pt(CN)_(4)]^(2-);TCP;CH_(2)Cl_(2)}supramolecular system(TCP-tetracyanopyrazine).In the solid-state,a mixture of needle-like co-crystals first appears,(PPh_(4))_(2){[TCP][Pt(CN)_(4)]}(1)and(PPh_(4))_(2){[TCP][Pt(CN)_(4)]}·2CH_(2)Cl_(2)(2),and subsequent recrystallization leads to block-shaped co-crystals of(PPh_(4))_(2){[TCP]2[Pt(CN)_(4)]}·2CH_(2)Cl_(2)(3),wherein double{[Pt(CN)_(4)]^(2-);TCP}and triple{[Pt(CN)_(4)]^(2-);TCP;CH_(2)Cl_(2)}and{PPh4^(+);[Pt(CN)_(4)]^(2-);TCP}synthons present either in 1 or 2 are reproduced in 3.The structural pathway(1,2→3)is accompanied by a 1D-to-2D modular evolution of anion-πinteractions between[Pt(CN)_(4)]^(2-)andπ-acidic TCP that seems to be driven,as indicated by calculations,not by maximizing their strength but rather by optimizing other crystal interactions,e.g.between PPh4^(+)cations.Formation of the corresponding{[Pt(CN)_(4)]^(2-);π-acid}anion-πcontacts in solution is evidenced by 13C NMR shifts and by new low-energy electronic absorption in the visible region(UV-vis).Finally,a combined solution/solid-state ^(195)Pt NMR approach is used for the first time to shed light on the geometry and interactions involving such aggregates;it shows that the degree of trapping of[Pt(CN)_(4)]^(2-)near aπ-acidic surface can be monitored by ^(195)Pt NMR chemical shifts.The results give fresh insight into block arrangement tactics and characterization of hybrid organic-inorganic co-crystal salts,and into aggregation controlled properties.展开更多
We evaluated nine plastid （matK, rbcL, rpoCl, rpoB, rp136-rpsS, ndhJ, trnL-F, tmrnH-psbA, accD） and two nuclear （ITS and ITS2） barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belongin...We evaluated nine plastid （matK, rbcL, rpoCl, rpoB, rp136-rpsS, ndhJ, trnL-F, tmrnH-psbA, accD） and two nuclear （ITS and ITS2） barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction （PCR） amplicons in all the accessions tested. However, only 35 （58%） and 4o accessions （66~） yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species （75%） into monophyletic groups and five species into two para- phyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species （6o%）, and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence ofnatural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of iTS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.展开更多
基金financially supported by the National Natural Science Foundation of China(Grant No.32060310)a grant from the Department of Education of Guangxi.
文摘The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines.However,few studies have investigated intraspecies mitogenomic variation.In this study,69 mitogenomes of the Black-throated Tit(Aegithalos concinnus)were assembled and annotated from a large number of short reads generated using high-throughput sequencing technology.Comparative analyses revealed that mitogenomic characteristics such as length,gene and nucleotide composition,codon usage,and duplicated control regions were relatively conserved despite substantial intraspecies morphological changes.Yet,all the individuals from the subspecies A.c.iredalei had one more nucleotide in the 12S rRNA than the other studied subspecies.Phylogenetic analyses showed five distinct lineages based on the complete mitogenomes and the 13 combined protein-coding genes,whereas only four lineages were observed when using the duplicate control regions.Most interestingly,each lineage had both copies of the control regions of the comprising individuals,indicating that the paralogous control regions were more similar than the orthologous sequences from the distinct lineages.This suggested the control regions had undergone concerted evolution.The Black-throated Tit has complex evolutionary history and needs further investigating the taxonomic status of these lineages,as well as the underlying evolutionary processes.Our findings call for more research on intraspecies mitogenomic variation.
基金supported by the National Science Center in Poland(grant OPUS 8,UMO 2014/15/B/ST5/02098)E.Kuzniak acknowledges the fellowship within the project no.POWR.03.02.00-00-I013/16.J.Hooper is grateful for the financial support from the Ministry of Science and Higher Education in Poland(Outstanding Young Scientist scholarship)+2 种基金R.Podgajny and S.Ferlay acknowledge the support from French Government and the French Embassy in Poland(the BGF Fellowship)Measurements were carried out with the equipment purchased thanks to the support of the European Regional Development Fund in the framework of the Polish Innovation Economy Operational Program(contract no.POIG.02.01.00-12-023/08)the PL-Grid Infrastructure and the ACC Cyfronet AGH(Krakow,Poland)for computational resources.
文摘Combined Single-Crystal XRD,solution 13C and ^(195)Pt NMR,solid-state ^(195)Pt NMR and UV-vis measurements,together with comprehensive(TD)DFT calculations,are used to describe the supramolecular interactions and sequential concerted structural transformation occurring in a{PPh4^(+);[Pt(CN)_(4)]^(2-);TCP;CH_(2)Cl_(2)}supramolecular system(TCP-tetracyanopyrazine).In the solid-state,a mixture of needle-like co-crystals first appears,(PPh_(4))_(2){[TCP][Pt(CN)_(4)]}(1)and(PPh_(4))_(2){[TCP][Pt(CN)_(4)]}·2CH_(2)Cl_(2)(2),and subsequent recrystallization leads to block-shaped co-crystals of(PPh_(4))_(2){[TCP]2[Pt(CN)_(4)]}·2CH_(2)Cl_(2)(3),wherein double{[Pt(CN)_(4)]^(2-);TCP}and triple{[Pt(CN)_(4)]^(2-);TCP;CH_(2)Cl_(2)}and{PPh4^(+);[Pt(CN)_(4)]^(2-);TCP}synthons present either in 1 or 2 are reproduced in 3.The structural pathway(1,2→3)is accompanied by a 1D-to-2D modular evolution of anion-πinteractions between[Pt(CN)_(4)]^(2-)andπ-acidic TCP that seems to be driven,as indicated by calculations,not by maximizing their strength but rather by optimizing other crystal interactions,e.g.between PPh4^(+)cations.Formation of the corresponding{[Pt(CN)_(4)]^(2-);π-acid}anion-πcontacts in solution is evidenced by 13C NMR shifts and by new low-energy electronic absorption in the visible region(UV-vis).Finally,a combined solution/solid-state ^(195)Pt NMR approach is used for the first time to shed light on the geometry and interactions involving such aggregates;it shows that the degree of trapping of[Pt(CN)_(4)]^(2-)near aπ-acidic surface can be monitored by ^(195)Pt NMR chemical shifts.The results give fresh insight into block arrangement tactics and characterization of hybrid organic-inorganic co-crystal salts,and into aggregation controlled properties.
基金financial support (BT/ PR8349/NDB/51/136/2006 19/01/2007–19-01/2010) from the Department of Biotechnology, Government of India
文摘We evaluated nine plastid （matK, rbcL, rpoCl, rpoB, rp136-rpsS, ndhJ, trnL-F, tmrnH-psbA, accD） and two nuclear （ITS and ITS2） barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction （PCR） amplicons in all the accessions tested. However, only 35 （58%） and 4o accessions （66~） yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species （75%） into monophyletic groups and five species into two para- phyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species （6o%）, and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence ofnatural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of iTS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.
