Soil bank analysis of weed seeds at farm Lužnica d.o.o.

Pojam „banka sjemena korova u tlu“ podrazumijeva svu količinu sjemena koja se nalazi u tlu i mjesto gdje se sjeme skuplja i ostaje do stvaranja povoljnih uvjeta za klijanje i nicanje. Poznavanjem sastava i količine sjemenki korova u banci sjemena može se predvidjeti buduća korovna flora na određenoj parceli i mogućnost planiranja, odnosno izrada strategije suzbijanja korova kao sastavni dio integrirane zaštite bilja. Cilj ovog istraživanja bio je utvrditi banku sjemena korova u tlu na gospodarstvu Lužnica d.o.o., Zaprešić. Metoda utvrđivanja banke sjemena bila je ispiranje i prosijavanje tla s ciljem dobivanja sjemenki korova iz pojedinog uzorka tla. Uzorci tla su uzeti pedološkom sondom za uzorkovanje neporemećenog profila tla na sljedećim dubinama: 0-10 cm, 10-20 cm, 20-30 cm i 30-40 cm. Uzorkovanje je obavljeno na pet mjesta na parceli prema “W“ shemi rasporeda. Daljnji proces analize banke sjemena obavljen je u laboratorijskim uvjetima u Zavodu za herbologiju. Metodom ispiranja uzoraka tla te determinacijom dobivenih korovnih sjemenki utvrđeno je da se banka sjemena korova na istraživanoj lokaciji sastoji od ukupno šest korovnih vrsta: Amaranthus retroflexus, Veronica persica, Sorghum halapense, Polygonum persicaria, Abutilon theophrasti i Ambrosia artemisiifolia. Najbrojnija korovna vrsta u banci sjemena je Amaranthus retroflexus koja je utvrđena na svim istraživanim dubinama. Ambrosia artemsiifolia nije utvrđena na dubinama 20-30 cm i 30-40 cm. Korovna flora na istraživanoj parceli, izuzev vrste Veronica persica, tipična je korovna flora okopavinskih kultura.The term “soil weed seed bank” defines all the quantity of the seeds that are found in soil and the place where the seeds are collected and where they remain until more favorable conditions for germination are occurred. Knowing the composition and quantity of the weed seeds in the seed bank, it is possible to predict future weed flora in the field and the possibility of planning or creating weed control strategy as a part of integrated weed management. The aim of this research was to determine the soil weed seed bank in soil of the farm Lužnica Ltd, Zaprešić. The seed bank method the was sieving of the soil in order to obtain weed seeds from each soil sample. The soil samples were taken with pedological sampling probe for undisturbed profile of the soil at the following depths: 0-10 cm, 10-20 cm, 20-30 cm, 30-40 cm. The soil sampling was carried out at five places in the parcel according to "W" scheme of arrangement. Further analysis of the seed bank was performed in the laboratory of the Department of Weed Science. Results show that the soil weed seeds bank on the examined site consisted of six weed species: Amaranthus retroflexus, Veronica persica, Sorghum halapense, Polygonum persicaria, Abutilon theophrasti and Ambrosia artemisiifolia. The most common weed species in the seed bank was Amaranthus retroflexus which had been found in all examined depths. Ambrosia artemisiifolia has not been established at the depths of 20-30 cm and 30-40 cm. Weed flora in the examined field, except for species Veronica persica, represents typical weed flora of row crops

Soil bank analysis of weed seeds at farm Lužnica d.o.o.

Pojam „banka sjemena korova u tlu“ podrazumijeva svu količinu sjemena koja se nalazi u tlu i mjesto gdje se sjeme skuplja i ostaje do stvaranja povoljnih uvjeta za klijanje i nicanje. Poznavanjem sastava i količine sjemenki korova u banci sjemena može se predvidjeti buduća korovna flora na određenoj parceli i mogućnost planiranja, odnosno izrada strategije suzbijanja korova kao sastavni dio integrirane zaštite bilja. Cilj ovog istraživanja bio je utvrditi banku sjemena korova u tlu na gospodarstvu Lužnica d.o.o., Zaprešić. Metoda utvrđivanja banke sjemena bila je ispiranje i prosijavanje tla s ciljem dobivanja sjemenki korova iz pojedinog uzorka tla. Uzorci tla su uzeti pedološkom sondom za uzorkovanje neporemećenog profila tla na sljedećim dubinama: 0-10 cm, 10-20 cm, 20-30 cm i 30-40 cm. Uzorkovanje je obavljeno na pet mjesta na parceli prema “W“ shemi rasporeda. Daljnji proces analize banke sjemena obavljen je u laboratorijskim uvjetima u Zavodu za herbologiju. Metodom ispiranja uzoraka tla te determinacijom dobivenih korovnih sjemenki utvrđeno je da se banka sjemena korova na istraživanoj lokaciji sastoji od ukupno šest korovnih vrsta: Amaranthus retroflexus, Veronica persica, Sorghum halapense, Polygonum persicaria, Abutilon theophrasti i Ambrosia artemisiifolia. Najbrojnija korovna vrsta u banci sjemena je Amaranthus retroflexus koja je utvrđena na svim istraživanim dubinama. Ambrosia artemsiifolia nije utvrđena na dubinama 20-30 cm i 30-40 cm. Korovna flora na istraživanoj parceli, izuzev vrste Veronica persica, tipična je korovna flora okopavinskih kultura.The term “soil weed seed bank” defines all the quantity of the seeds that are found in soil and the place where the seeds are collected and where they remain until more favorable conditions for germination are occurred. Knowing the composition and quantity of the weed seeds in the seed bank, it is possible to predict future weed flora in the field and the possibility of planning or creating weed control strategy as a part of integrated weed management. The aim of this research was to determine the soil weed seed bank in soil of the farm Lužnica Ltd, Zaprešić. The seed bank method the was sieving of the soil in order to obtain weed seeds from each soil sample. The soil samples were taken with pedological sampling probe for undisturbed profile of the soil at the following depths: 0-10 cm, 10-20 cm, 20-30 cm, 30-40 cm. The soil sampling was carried out at five places in the parcel according to "W" scheme of arrangement. Further analysis of the seed bank was performed in the laboratory of the Department of Weed Science. Results show that the soil weed seeds bank on the examined site consisted of six weed species: Amaranthus retroflexus, Veronica persica, Sorghum halapense, Polygonum persicaria, Abutilon theophrasti and Ambrosia artemisiifolia. The most common weed species in the seed bank was Amaranthus retroflexus which had been found in all examined depths. Ambrosia artemisiifolia has not been established at the depths of 20-30 cm and 30-40 cm. Weed flora in the examined field, except for species Veronica persica, represents typical weed flora of row crops

The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles

International audienceThe complete mitochondrial genome of the recently discovered beetle family Iberobaeniidae is described and compared with known coleopteran mitogenomes. The mitochondrial sequence was obtained by shotgun metagenomic sequencing using the Illumina Miseq technology and resulted in an average coverage of 130 × and a minimum coverage of 35×. The mitochondrial genome of Iberobaeniidae includes 13 protein-coding genes, 2 rRNAs, 22 tRNAs genes, and 1 putative control region, and showed a unique rearrangement of protein-coding genes. This is the first rearrangement affecting the relative position of protein-coding and ribosomal genes reported for the order Coleoptera

Family-level sampling of mitochondrial genomes in coleoptera: compositional heterogeneity and phylogenetics

Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be sampled more densely. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5 and nad6 genes. Credible tree topologies were obtained with the nhPhyML (‘non-homogeneous’) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher-level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia (Staphyliniformia + Scarabaeiformia (Bostrichiformia (Cucujiformia)))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, whilst compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees

Family-Level Sampling of Mitochondrial Genomes in Coleoptera : Compositional Heterogeneity and Phylogenetics

Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5, and nad6 genes. Credible tree topologies were obtained with the nhPhyML ("nonhomogeneous") algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.Peer reviewe

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags (‘barcodes’). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three ‘bait’ sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species ‘barcodes’ that currently use the cox1 gene only

Firefly genomes illuminate parallel origins of bioluminescence in beetles

Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of bioluminescence within beetles remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. To compare bioluminescent origins, we also sequenced the genome of a related click beetle, the Caribbean Ignelater luminosus, with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing hypothesis of parallel gains of bioluminescence. Our analyses support independent gains of bioluminescence in fireflies and click beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle

Cladophorus haiaensis Bocak 2017, sp. nov.

<i>Cladophorus haiaensis</i> sp. nov. <p>(Figs. 9, 19, 23, 39, 59–60)</p> <p> <b>Type material</b>. Holotype, male. Papua New Guinea, Crater Mt., Haia, Supa, 06°40´S 145°03´E, 1070–1450 m (A00124, LMBC).</p> <p> <b>Diagnosis.</b> <i>C. haiaensis</i> has a smaller body compared with other <i>Cladophorus</i> and it is the only uniformly black coloured species. The species represents the deepest split in the genus (Fig. 4) and the different shape of the phallus supports its position (Figs. 59–60). Although having slightly different genitalia, <i>C. haiaensis</i> is robustly placed in <i>Cladophorus</i> (BS 88%) and the morphological divergence is limited to genitalia, which are under strong sexual selection.</p> <p> <b>Description.</b> Male. Body small, 10.0 mm long, uniformly dark brown to black (Fig. 39). Head small, with very small eyes, frontal interocular distance 2.37 times maximum diameter; antennae long, reaching beyond half of elytral length, flabellate, antennomere 3 with lamella attached to apical part of antennomere (Fig. 9), but its apical part missing in holotype, antennomeres 7–9 with very long lamellae (Fig. 19). Pronotum transverse, much wider basally, 1.57 times wider than long at midline, lateral margins slightly elevated, frontal margin slightly rounded, frontal angles obtuse but conspicuous, lateral margins straight, posterior angles sharply prominent, postero-lateral carinae weak in middle of disc and antero-lateral carinae weak towards frontal margin, median anterior carina welldeveloped (Fig. 23). Elytra flat, only slightly widened posteriorly, transverse costae weak, irregular, partly covered by pubescence, elytral areoles variable in shape (Fig. 39). Phallus very slender, widest basally, narrowed gradually to apex (Figs. 59–60).</p> <p> <b>Measurements.</b> BL 10.0 mm, PL 1.12 mm, PW 1.67 mm, WH 1.06 mm, Edist 0.83 mm, Ediam 0.35 mm, LE 8.5 mm, antennomere 3: measurements unavailable.</p> <p> <b>Distribution.</b> Eastern New Guinea, Chimbu province (Fig. 3).</p> <p> <b>Etymology.</b> The epithet refers to the local name ‘Haia’, the type locality of the species.</p>Published as part of <i>Bocak, Ladislav, 2017, Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea, pp. 505-522 in Zootaxa 4320 (3)</i> on pages 511-512, DOI: 10.11646/zootaxa.4320.3.6, <a href="http://zenodo.org/record/1051951">http://zenodo.org/record/1051951</a&gt