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Variation of and associations with the depth and evenness of sequencing coverage in a sample of archived plastid genomes
<p>Depth and evenness of sequencing coverage are considered potential indicators of genome assembly quality. In plastid genomics, where new data generation has outpaced the development of suitable assembly quality indicators, these coverage metrics could offer insights into the quality of plastomes of different sizes, structures, or taxonomic origins. However, the typical variation of sequencing depth and evenness among archived plastid genomes, their variability between plastome partitions, and any association with methodological factors have yet to be evaluated. This study explores the variation of sequencing depth and evenness across a sample of publicly accessible plastid genomes and their potential associations with plastome structure, assembly accuracy, and the methodological provenance of the genome data using statistical tests. Our results indicate significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides, and a significant difference in sequencing evenness between several DNA sequencing platforms. These findings highlight that many publicly accessible plastid genomes are based on sequence data with highly variable sequencing depth and evenness and that this variation is influenced, at least partially, by genome structure and methodological factors.</p>
Appendix 2 in A new subfamily classification of the Citrus family (Rutaceae) based on six nuclear and plastid markers
<p><b>Appendix 2.</b> Details about the character states of all included taxa for the 13 morphological and karyological characters.</p><table><thead><tr><th></th><th></th><th></th><th></th><th></th><th></th><th colspan="2">Characters</th><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><th>Taxon</th><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td colspan="2">6 7</td><td>8</td><td>9</td><td>10</td><td>11</td><td>12</td><td>13</td></tr><tr><th><i>Acmadenia</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Acradenia</i></th><td>1</td><td>1</td><td>2, 3</td><td>1</td><td>1</td><td>1</td><td>2</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Acronychia</i></th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>1</td><td>1</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Adenandra</i></th><td>0</td><td>0, 1</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>2, 3</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Adiscanthus</i></th><td>0</td><td>0</td><td>2</td><td>0</td><td>0</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Aegle</i></th><td>0, 1</td><td>0</td><td>1, 2</td><td>2</td><td>0</td><td>4</td><td>0</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Aeglopsis</i></th><td>0, 1</td><td>0</td><td>1, 2, 3</td><td>1, 2</td><td>0</td><td>4</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Afraegle</i></th><td>1</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>4</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Agathosma</i> A</th><td>0</td><td>0, 1, 2</td><td>2, 3</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Agathosma</i> B</th><td>0</td><td>0, 1, 2</td><td>2, 3</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Agathosma</i> C</th><td>0</td><td>0, 1, 2</td><td>2, 3</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Amyris</i></th><td>0, 1</td><td>0, 1</td><td>1, 2, 3</td><td>1</td><td>3</td><td>1</td><td>1</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Andreadoxa</i></th><td>0</td><td>0</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>1</td><td>0</td><td>0</td></tr><tr><th><i>Angostura</i></th><td>0, 1</td><td>0</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0, 1</td><td>1</td><td>0</td></tr><tr><th><i>Asterolasia</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>0, 1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Atalantia</i></th><td>0</td><td>0</td><td>1, 2, 3</td><td>1</td><td>0</td><td>0, 1</td><td>5</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Balfourodendron</i></th><td>1</td><td>1</td><td>1</td><td>0</td><td>0</td><td>1</td><td>4</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Balsamocitrus</i></th><td>0, 1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>4</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Bergera</i></th><td>0, 1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>?</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Boenninghausenia</i></th><td>1</td><td>0</td><td>1</td><td>1</td><td>1</td><td>2, 3</td><td>2</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Boronia</i> A</th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>0, 1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Boronia</i> B</th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>0, 1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Boronia</i> C</th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>0, 1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Boronia</i> D (<i>Boronella</i>)</th><td>0</td><td>1, 2</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Bosistoa</i></th><td>0, 1</td><td>0</td><td>2</td><td>1</td><td>1</td><td>2, 3</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Bottegoa</i></th><td>1</td><td>0</td><td>1, 2</td><td>0</td><td>0</td><td>0</td><td>4</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Bouchardatia</i></th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>3</td><td>2</td><td>0, 1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Brombya</i></th><td>0</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Burkillanthus</i></th><td>0, 1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>4</td><td>5</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Calodendrum</i></th><td>0</td><td>1, 2</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Casimiroa</i></th><td>0, 1</td><td>0</td><td>1, 2, 3</td><td>0</td><td>0</td><td>1, 2, 3</td><td>0, 1</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Cedrelopsis</i></th><td>1</td><td>0</td><td>2</td><td>0</td><td>0</td><td>1, 2</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Chloroxylon</i></th><td>1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>3</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Choisya</i></th><td>1</td><td>1</td><td>1, 2</td><td>1</td><td>1</td><td>1</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Chorilaena</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Citropsis</i></th><td>0, 1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>0</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Citrus</i> A</th><td>0</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Citrus</i> B</th><td>0</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th>Taxon</th><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td colspan="2">Characters 6 7</td><td>8</td><td>9</td><td>10</td><td>11</td><td>12</td><td>13</td></tr><tr><th><i>Citrus</i> C</th><td>0</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Clausena</i></th><td>1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Clymenia</i> (<i>Citrus</i> s.l.)</th><td>0</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Cneoridium</i></th><td>0</td><td>1</td><td>1</td><td>1</td><td>3</td><td>1, 2</td><td>0</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Cneorum</i></th><td>0</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Coatesia</i></th><td>0</td><td>0</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Coleonema</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Comptonella</i></th><td>0, 1</td><td>1</td><td>1</td><td>0, 1</td><td>0, 1</td><td>1</td><td>1</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Conchocarpus</i> A</th><td>0, 1</td><td>0, 1</td><td>1, 2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0, 1</td><td>1</td><td>0</td></tr><tr><th><i>Conchocarpus</i> B (<i>Almeidea</i>)</th><td>0</td><td>0</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Correa</i></th><td>0</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>1</td><td>0</td></tr><tr><th><i>Crossosperma</i></th><td>1</td><td>1</td><td>1</td><td>1</td><td>0</td><td>0, 1</td><td>1</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Crowea</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Cyanothamnus</i></th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Desmotes</i></th><td>0</td><td>1</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>Dictamnus</i></th><td>1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>2</td><td>2</td><td>2</td><td>1</td><td>2</td><td>1</td><td>0</td><td>0</td></tr><tr><th><i>Dictyoloma</i></th><td>1</td><td>0</td><td>2</td><td>0</td><td>1</td><td>2</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Dinosperma</i></th><td>0, 1</td><td>0, 1, 2</td><td>1</td><td>1</td><td>1</td><td>1</td><td>2</td><td>0, 1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Diosma</i></th><td>0</td><td>0, 1</td><td>2</td><td>0, 1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Diplolaena</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Drummondita</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Dryades</i></th><td>0</td><td>0</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>?</td><td>?</td><td>0</td><td>0, 1</td><td>1</td><td>0</td></tr><tr><th><i>Dutaillyea</i></th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>0</td><td>0, 1</td><td>1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Empleurum</i></th><td>0</td><td>0</td><td>1</td><td>0</td><td>1, 3</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Eremocitrus</i> (<i>Citrus</i> s.l.)</th><td>0</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Eriostemon</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Ertela</i></th><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>1, 2</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>Erythrochiton</i></th><td>0</td><td>0</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0, 1</td><td>1</td><td>0</td></tr><tr><th><i>Esenbeckia</i></th><td>0, 1</td><td>0, 1</td><td>2, 3</td><td>0</td><td>0, 1</td><td>1</td><td>2</td><td>0, 1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Euchaetis</i></th><td>0</td><td>0, 1</td><td>2</td><td>0, 1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Euodia</i></th><td>0, 1</td><td>1</td><td>1</td><td>0, 1</td><td>1</td><td>1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Fagaropsis</i></th><td>1</td><td>1</td><td>1, 2, 3</td><td>0, 1</td><td>0</td><td>0</td><td>1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Feroniella</i></th><td>1</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Flindersia</i></th><td>0, 1</td><td>0, 1</td><td>2</td><td>1</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 3</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Fortunella</i> (<i>Citrus</i> s.l.)</th><td>0</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Galipea</i></th><td>0, 1</td><td>0</td><td>2</td><td>0</td><td>0</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>Geijera</i></th><td>0</td><td>0</td><td>0, 1, 2</td><td>0</td><td>1</td><td>1</td><td>3</td><td>1</td><td>3</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Geleznowia</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Glycosmis</i></th><td>0, 1</td><td>0</td><td>1, 2</td><td>0, 1</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>0, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Halfordia</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>0</td><td>0</td><td>1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Haplophyllum</i></th><td>0, 1</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1, 2, 3</td><td>2</td><td>2</td><td>0</td><td>1, 2</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Harrisonia</i></th><td>1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>0</td><td>1</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Helietta</i></th><td>1</td><td>0, 1</td><td>1, 2</td><td>0</td><td>0</td><td>1</td><td>4</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Hortia</i></th><td>0</td><td>0</td><td>2</td><td>0</td><td>0</td><td>1</td><td>0, 1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th>Taxon</th><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td colspan="2">Characters 6 7</td><td>8</td><td>9</td><td>10</td><td>11</td><td>12</td><td>13</td></tr><tr><th><i>Ivodea</i></th><td>0</td><td>0, 1, 2</td><td>1, 2</td><td>0, 1</td><td>1</td><td>1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Leionema</i> A</th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0, 1</td><td>0</td></tr><tr><th><i>Leionema</i> B</th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0, 1</td><td>0</td></tr><tr><th><i>Limonia</i></th><td>1</td><td>0</td><td>1, 2, 3</td><td>1</td><td>0</td><td>4</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Lunasia</i></th><td>0</td><td>0</td><td>0</td><td>0</td><td>1</td><td>0</td><td>2</td><td>0, 1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Luvunga</i></th><td>0, 1</td><td>0</td><td>0, 1, 2</td><td>1</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Maclurodendron</i></th><td>0</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Macrostylis</i></th><td>0</td><td>0, 1</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Medicosma</i></th><td>0, 1</td><td>0, 1, 2</td><td>1</td><td>0, 1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Melicope</i> A</th><td>0, 1</td><td>1</td><td>1</td><td>0, 1</td><td>1</td><td>1</td><td>3</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Melicope</i> B</th><td>0, 1</td><td>1</td><td>1</td><td>0</td><td>0, 1</td><td>1</td><td>3</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Melicope</i> C</th><td>0, 1</td><td>1, 2</td><td>1</td><td>0, 1</td><td>0, 1</td><td>1</td><td>3</td><td>2</td><td>0, 1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Melicope</i> D</th><td>0, 1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>0, 1</td><td>3</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Melicope</i> E (<i>Platydesma</i>)</th><td>0</td><td>0, 1</td><td>1</td><td>1</td><td>0</td><td>2, 3</td><td>3</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Merope</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>0</td><td>1, 2</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Merrillia</i></th><td>1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>?</td><td>0</td><td>1</td><td>0</td><td>0</td></tr><tr><th><i>Metrodorea</i></th><td>0, 1</td><td>1</td><td>2</td><td>0</td><td>0</td><td>1</td><td>2</td><td>0, 1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Microcitrus</i> (<i>Citrus</i> s.l.)</th><td>0</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Microcybe</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Micromelum</i></th><td>0, 1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Monanthocitrus</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>0</td><td>1, 2, 3</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Muiriantha</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>1</td><td>0</td></tr><tr><th><i>Murraya</i></th><td>1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Myrtopsis</i></th><td>0</td><td>1</td><td>1, 2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>?</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Naringi</i></th><td>0, 1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>0, 1</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Nematolepis</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0, 1</td><td>0</td></tr><tr><th><i>Neobyrnesia</i></th><td>0</td><td>1</td><td>1</td><td>0</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Neoraputia</i></th><td>0, 1</td><td>0, 1</td><td>2</td><td>0</td><td>0</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>Neoschmidea</i></th><td>0</td><td>0</td><td>1, 2</td><td>1</td><td>1</td><td>1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Orixa</i></th><td>0</td><td>0</td><td>1</td><td>0</td><td>1</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Pamburus</i></th><td>0</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Paramignya</i></th><td>0</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Peltostigma</i></th><td>0, 1</td><td>0</td><td>0, 1, 2, 3</td><td>1, 2</td><td>0</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Pentaceras</i></th><td>1</td><td>0</td><td>2</td><td>1</td><td>1</td><td>1</td><td>1, 4</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Perryodendron</i></th><td>0</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>3</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Phebalium</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Phellodendron</i></th><td>1</td><td>1</td><td>2</td><td>0</td><td>0</td><td>0</td><td>1</td><td>1</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Philotheca</i> A</th><td>0</td><td>0</td><td>1, 2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1, 2</td><td>0</td><td>0</td><td>0, 1</td><td>0</td></tr><tr><th><i>Philotheca</i> B</th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1, 2</td><td>0</td><td>0</td><td>0, 1</td><td>0</td></tr><tr><th><i>Phyllosma</i></th><td>0</td><td>0</td><td>2</td><td>0, 1</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Picrella</i></th><td>0, 1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0, 1</td><td>1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Pilocarpus</i></th><td>0, 1</td><td>0</td><td>1, 2</td><td>0</td><td>0</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Pitavia</i></th><td>0</td><td>1, 2</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Pitaviaster</i></th><td>0</td><td>1</td><td>1</td><td>0</td><td>1</td><td>1</td><td>1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th>Taxon</th><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td colspan="2">Characters 6 7</td><td>8</td><td>9</td><td>10</td><td>11</td><td>12</td><td>13</td></tr><tr><th><i>Pleiospermium</i></th><td>0, 1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>1</td><td>5</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Plethadenia</i></th><td>1</td><td>0, 1</td><td>1</td><td>1</td><td>2</td><td>0</td><td>2</td><td>?</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Poncirus</i> (<i>Citrus</i> s.l.)</th><td>1</td><td>0</td><td>1, 2, 3</td><td>2</td><td>0</td><td>1, 2, 3</td><td>5</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Psilopeganum</i></th><td>1</td><td>0</td><td>1, 2</td><td>1</td><td>1</td><td>2, 3</td><td>2</td><td>2</td><td>?</td><td>2</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Ptaeroxylon</i></th><td>1</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Ptelea</i></th><td>1</td><td>0</td><td>1, 2, 3</td><td>0</td><td>0</td><td>1</td><td>2, 4</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Rauia</i></th><td>0, 1</td><td>0</td><td>2</td><td>0</td><td>0</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0</td><td>1</td><td>0</td></tr><tr><th><i>Ravenia</i></th><td>0, 1</td><td>1</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>Rhadinothamnus</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0, 1</td><td>0</td></tr><tr><th><i>Ruta</i></th><td>1</td><td>0</td><td>1, 2</td><td>1</td><td>0</td><td>4</td><td>2</td><td>2</td><td>0, 1, 2</td><td>1, 2</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Sarcomelicope</i></th><td>0</td><td>1, 2</td><td>1</td><td>1</td><td>0, 1</td><td>1</td><td>1</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Severinia</i></th><td>0</td><td>0</td><td>1, 2, 3</td><td>1</td><td>0</td><td>0, 1</td><td>5</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Sheilanthera</i></th><td>0</td><td>0</td><td>2</td><td>0</td><td>1</td><td>0, 1</td><td>2</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Sigmatanthus</i></th><td>1</td><td>0</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>Skimmia</i></th><td>0</td><td>0</td><td>1, 2, 3</td><td>0</td><td>0</td><td>0</td><td>1</td><td>2</td><td>1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Sohnreyia</i></th><td>1</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0, 1</td><td>4</td><td>0, 1, 2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Spathelia</i></th><td>1</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0, 1</td><td>4</td><td>0, 1, 2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Spiranthera</i></th><td>1</td><td>0</td><td>2</td><td>0</td><td>0</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Swinglea</i></th><td>1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>4</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Tetractomia</i></th><td>0</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>3</td><td>2</td><td>?</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Tetradium</i></th><td>1</td><td>1</td><td>1, 2</td><td>0</td><td>1</td><td>0, 1</td><td>3</td><td>2</td><td>1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Thamnosma</i></th><td>0</td><td>0</td><td>1</td><td>1</td><td>0</td><td>2, 3</td><td>2</td><td>2</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Toxosiphon</i></th><td>0, 1</td><td>0</td><td>2</td><td>0</td><td>0</td><td>1</td><td>2</td><td>1</td><td>?</td><td>0</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>Triphasia</i></th><td>0, 1</td><td>0</td><td>0, 2</td><td>1</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>0, 1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Vepris</i></th><td>0, 1</td><td>0, 1</td><td>1</td><td>0, 1</td><td>0, 3</td><td>0, 1</td><td>1</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Wenzelia</i></th><td>0</td><td>0</td><td>2</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>?</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Zanthoxylum</i> A</th><td>0, 1</td><td>0</td><td>1, 2</td><td>0</td><td>1</td><td>1</td><td>3</td><td>1, 2</td><td>1, 2, 3</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Zanthoxylum</i> B</th><td>0, 1</td><td>0</td><td>1, 2</td><td>0</td><td>1</td><td>1</td><td>3</td><td>1, 2</td><td>1, 2, 3</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Zanthoxylum</i> C</th><td>0, 1</td><td>0</td><td>0, 1, 2, 3</td><td>0</td><td>1</td><td>1</td><td>3</td><td>1, 2</td><td>1, 2, 3</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Zanthoxylum</i> D (<i>Toddalia</i>)</th><td>0, 1</td><td>0</td><td>1, 2, 3</td><td>0</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Zieria</i></th><td>0, 1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>0, 1</td><td>2</td><td>2</td><td>1, 2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr></tbody></table><p><b>1.</b> Leaf type: (0) simple/unifoliolate; (1) compound. <b>2.</b> Phyllotaxis: (0) alternate; (1) opposite; (2) whorled. <b>3.</b> Flower merosity: (0) 3-merous; (1) 4-merous; (2) 5-merous; (3) polymerous. <b>4.</b> Stamen whorls: (0) haplostemonous; (1) diplostemonous; (2) more than two whorls. <b>5.</b> Carpel connation: (0) syncarpous; (1) syncarpous (style only); (2) apocarpous (no joined style); (3) one carpel. <b>6.</b> Ovules per locule: (0) 1; (1) 2; (2) 3–5; (3) 6–10; (4)>10. <b>7.</b> Fruit type: (0) berry; (1) drupe; (2) dehiscent with seeds detached; (3) dehiscent with seeds attached; (4) samara; (5) hesperidium. <b>8.</b> Endosperm: (0) lacking; (1) scanty; (2) copious. <b>9.</b> Chromosomes: (0) 9–10; (1) 14–18; (2) 28–36; (3) ≥64. <b>10.</b> Growth form: (0) shrubs or trees; (1) subshrubs; (2) perennial herbs. <b>11.</b> Flower symmetry: (0) actinomorphic; (1) zygomorphic. <b>12.</b> Tubular corolla: (0) petals free and not forming a tube; (1) petals coherent or connate and forming a corolla tube. <b>13.</b> Seeds: (0) not winged; (1) winged</p><p>(Continues)</p><p>(Continues)</p>
Data from: A multi-locus plastid phylogeny of the Aulonemia clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) reveals three new genera of bamboo
<p>Arthrostylidiinae (Poaceae: Bambusoideae), a subtribe of Neotropical woody bamboos with diverse morphology, comprises 200 species classified in 16 genera. Previous studies supported monophyly of the subtribe and recovered four major internal clades, however, some genera were found to be polyphyletic while others, like <em>Aulonemia</em> and <em>Colanthelia,</em> were either undersampled or not included. <em>Aulonemia</em> and <em>Colanthelia</em> are complex both in their taxonomy and morphology, and exhibit overlapping morphological characters. Prior morphological and molecular analyses suggested they share a close relationship, with <em>Colanthelia </em>emerging as monophyletic and either nested within <em>Aulonemia</em> or sister to it,<em> </em>but these studies sampled relatively few species of each genus. The aims of this study were to increase taxon sampling to test the monophyly of <em>Aulonemia</em> and <em>Colanthelia, </em>to investigate the relationships within the <em>Aulonemia </em>+ <em>Colanthelia </em>clade, and to revise their classification as appropriate towards a natural classification of the Arthrostylidiinae. We present a multi-locus plastid phylogeny of the Arthrostylidiinae with emphasis on <em>Aulonemia </em>and <em>Colanthelia</em>. We used sequences of seven plastid markers (one coding: <em>ndhF</em>; six non-coding:<em> trnC-rpoB, rps16-trnQ, trnT-trnL, rps16, trnD-trnT, </em>and <em>rpl16</em>) from 67 taxa of Bambusoideae including all genera of Arthrostylidiinae. Phylogenetic trees were inferred using both Bayesian and maximum likelihood methods. <em>Aulonemia</em> was confirmed as polyphyletic and <em>Colanthelia</em> was not supported as monophyletic. The phylogenetic position of <em>Myriocladus </em>within Arthrostylidiinae is resolved for the first time. All species of <em>Colanthelia</em> were recovered within the clade containing most species of <em>Aulonemia</em>. Four species of <em>Aulonemia</em> (<em>A. radiata</em>, <em>A. effusa</em>, <em>A. setosa</em>, and <em>A. setigera</em>) grouped in other clades within the subtribe and these placements combined with morphological evidence support the establishment of three new genera: <em>Quixiume</em>, <em>Stelanemia</em> and <em>Vianaea</em>, to accommodate the four remarkable <em>Aulonemia</em> species. An updated key for the genera of the Arthrostylidiinae is provided, as well as taxonomic treatments for the three new genera, including the description of a new species in <em>Stelanemia</em>.</p>
Figures 98–106. Stricosus and Thalassiosira. Figs 98–103. Stricosus harrisonii. Figs 98, 99. Living cells showing plastids with pyrenoids. Figs 100, 101 in Marine benthic diatoms of Guam: new records, Dictyoneis apapae sp. nov., and updates to the checklist
Figures 98–106. Stricosus and Thalassiosira. Figs 98–103. Stricosus harrisonii. Figs 98, 99. Living cells showing plastids with pyrenoids. Figs 100, 101. Acid cleaned valves in LM and SEM. Fig. 102. External apex showing triangular hyaline area, two spines, rimoportula opening, and ocellulimbus with at least 7 rows of pores (contrast Fig. 62, Hyalosynedra). Fig. 103. Apex internal view showing symmetrical rimoportula (arrow). Figs 104–106. Thalassiosira nanolineata. Fig. 104. Valve in LM at two focal planes. Fig. 105, 106. External and internal aspects in SEM, showing central fultoportulae (F) and rimoportula (R) (arrows). Scale bars: Figs 98, 100, 101 = 20 µm, Fig 104 = 10 µm, Figs 99, 103, 105, 106 = 5 µm, Fig. 102 = 2 µm.
Fig. 3 in Plastid genome of Aster altaicus var. uchiyamae Kitam., an endanger species of Korean asterids
Fig. 3. Comparison of chloroplast genomes of Aster altaicus var. uchiyamae and A. spathulifolius using mVISTA program. Grey arrows and thick black lines above the alignment indicate genes with their orientation and the position of the IRs, respectively. The Y-scale represents the percent identity between 50-100%. Genome regions are color-coded: Coding regions in blue; noncoding sequences (CNS) in red.
Text-fig. 2. Representative most parsimonious trees obtained after addition of Liliacidites to (A) the D&E tree (Text-fig. 1) and (B) the J/M tree, with relationships among major clades based on the plastid genome analyses of Jansen et al. (2007) and Moore et al. (2007). Thicker lines indicate all most parsimonious (MP), one step less parsimonious (MP+1), and two step less parsimonious (MP+2) positions for Liliacidites. Abbreviations as in Text-fig. 1. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 2. Representative most parsimonious trees obtained after addition of Liliacidites to (A) the D&E tree (Text-fig. 1) and (B) the J/M tree, with relationships among major clades based on the plastid genome analyses of Jansen et al. (2007) and Moore et al. (2007). Thicker lines indicate all most parsimonious (MP), one step less parsimonious (MP+1), and two step less parsimonious (MP+2) positions for Liliacidites. Abbreviations as in Text-fig. 1.
plastid:v24.8.1
<p>kraken2 DB for plastids built with masking option. Contains 15240 accession numbers corresponding to 15223 unique taxons.</p>
Fig. 5 in A new subfamily classification of the Citrus family (Rutaceae) based on six nuclear and plastid markers
Fig. 5. Ancestral state reconstruction for the characters growth form, flower symmetry, corolla tube, and winged vs. unwinged seeds. See Fig. 2 for taxon names.
Fig. 2 in A new subfamily classification of the Citrus family (Rutaceae) based on six nuclear and plastid markers
Fig. 2. Phylogenetic reconstruction of Rutaceae. The Bayesian 50% majority-rule consensus tree based on the concatenated alignments of all six markers is shown. Posterior probability (PP) and bootstrap (BS) support values are displayed next to each branch. Strongly supported branches are marked with an asterisk (*), branches with moderate and low support in the ML analyses are represented by a degree symbol (°) and a hash key (#) respectively. A hyphen (-) indicates branches that lack statistical support.
Fig. 1 in A new subfamily classification of the Citrus family (Rutaceae) based on six nuclear and plastid markers
Fig. 1. Diversity of flowers and fruits in Rutaceae. A, Trimerous and haplostemonous flower of Cneorum tricoccon L.; B, Tetramerous and diplostemonous flower of Ruta graveolens L.; C, Pentamerous and diplostemonous flower of Philotheca verrucosa (A.Rich.) Paul G.Wilson; D, Pentamerous and polystemonous flower of Citrus trifoliata L.; E, Zygomorphic flower of Dictamnus albus L.; F, Zygomorphic flower of Ravenia spectabilis (Lindl.) Planch. ex Griseb.; G, Tubular flower with connate petals of Correa lawrenceana Hook.; H, Inconspicuous flowers with tepals of the apomictic Zanthoxylum simulans Hance; I, Pendulous, capitate inflorescence with showy bracts of Diplolaena grandiflora Desf.; J, Baccate fruit of Triphasia trifolia (Burm.f.) P.Wilson; K, Capsular fruit of Melicope clusiifolia (A.Gray) T.G.Hartley & B.C.Stone, in which seeds remain attached to the carpels; L, Capsular fruit of Dictamnus albus L., in which seeds are ejected at maturity; M, Drupaceous fruit of Acronychia brassii T.G.Hartley; N, Young winged drupes of Spathelia splendens Urb.; O, Samaroid fruit of Ptelea trifoliata L.; P, Capsular fruit of Flindersia australis R.Br. — All photos by Marc S. Appelhans, except (F) by Milton Groppo and (P) by Paul I. Forster.
Fig. 4 in A new subfamily classification of the Citrus family (Rutaceae) based on six nuclear and plastid markers
Fig. 4. Ancestral state reconstruction for the characters ovules per locule, fruit type, presence of endosperm, and chromosome number. Dashed gray lines indicate unknown character states. See Fig. 2 for taxon names.
FIGURE 3 in Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
FIGURE 3. Summary of nuclear–plastid phylogenomic incongruence based on PACo analysis across different taxonomic levels between clades of Epidendroideae based on nuclear and plastid ML trees. Conflicting positions between orchid (A) genera, (B) subtribes, and (C) tribes. Association of terminals found to be incongruent and placed with robust support in nuclear and plastid trees are highlighted in bold and red. Pie diagrams at nodes represent quartet support values. Likelihood bootstrap support (LBS) percentages at nodes are 100 unless shown otherwise (LBS <85 are highlighted in red). Photos: Representatives of three strongly conflicting groups in the orchid family (Epidendreae: Pleurothallis perryi.; Catasetinae: Cycnoches guttulatum with its potential orchid bee pollinator (Euglossa aff. cybelia); Angraecinae: Angraecum rutenbergianum). Photo credits: O. A. Pérez-Escobar.
FIGURE 1 in Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
FIGURE 1. Split network of Orchidaceae computed from uncorrected p-distances and a supermatrix of 292 low-copy nuclear genes and 75 species. Splits are color-coded by orchid subfamily (see legend). Box on left: Taxonomic representativeness of orchid genera, tribes and subtribes sampled by nuclear gene datasets in this study. (Inset): Iconic representatives of different tribes in the orchid family (Vanilloideae: Vanilla inodora, Cleistes rosea; Cypripedioideae: Paphiopediluminsigne; Orchidoideae-Cranichideae:Ludisia discolor, Disa uniflora; Orchidoideae-Orchideae:Disa uniflora; Malaxidae: Dendrobium nobile; Epidendreae: Pleurothallis perryi and Scaphosepalum verrucosum; Cymbidieae: Zygopetalum crinitum and Maxillaria pereziana; Vandeae: Angraecum rutenbergianum). Photo credits: O. A. Pérez-Escobar and Sebastian Vieira.
Data from: Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics
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Plastid and peroxisome movement tracks in the root cells of Arabidopsis thaliana
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Phylogenomic insights into the origin of primary plastids
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Plastid-nuclear ERCnet analysis results
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Data from: A multi-locus plastid phylogeny of the Aulonemia clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) reveals three new genera of bamboo
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Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae
<p>Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding datasets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support, and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevents the confident resolution of these nodes using plastome data alone.</p>
Data from: NOVOWrap: an automated solution for plastid genome assembly and structure standardization
<p>Plastid genomes play an important role in genomics and evolutionary biology. Next-generation sequencing has revolutionized plastid genomic data acquisition to the point that genome assembly has become a bottlenecks for widespread utilization of plastid genome data. To solve this problem, we developed an open-source, cross-platform tool known as, NOVOWrap, which includes both command-line and graphical interfaces for automatically assembling plastid genomes on personal computers. With minimal inputs, settings, and user intervention, NOVOWrap can automatically assemble plastid genomes, validate results and standardize the structure using affordable computer resources. The performance of this software has been successfully benchmarked against the plastid genomes of 11 species belonging to lycopods, gymnosperms, and angiosperms. This program is expected to liberate researchers from laborious and cumbersome computer manipulations and create reliable and standardized genomic data.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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