On-chip synchronous pumped χ(3)\chi^{(3)} optical parametric oscillator on thin-film lithium niobate

Optical parametric oscillation (OPO) has widely been utilized as a means of generating light with wide spectral coverage from a single pump laser. These oscillators can be driven using either continuous-wave (CW) light, which only requires lining up of the pump frequency with OPO resonance, or pulsed light, which also mandates that the repetition rate of the pulse and free spectral range of the OPO cavity are carefully tuned to match each other. Advancements in nanophotonics have ignited interest in chip-scale OPOs, which enable low-footprint and high-efficiency solutions to broadband light generation. CW-pumped integrated OPO has been demonstrated using both $\chi^{(2)}$ and $\chi^{(3)}$ parametric oscillation. However, realizing pulse-driven on-chip OPO remains challenging, as microresonator cavities have limited tuning range in the FSR and resonance frequency compared to traditional bulk cavities. Here, we overcome this limitation and demonstrate a $\chi^{(3)}$ pulse-driven OPO by using a tunable on-chip femtosecond pulse generator to synchronously pump the oscillator. The output frequency comb generated by our OPO has 30-GHz repetition rate, spans 2/5 of an octave and consists of over 1400 comb lines with a pump-to-comb conversion efficiency of 10%

Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales

<div><p>Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Variable plastid genome sizes and extensive genome rearrangements have been observed across the diatom phylogeny, but little is known about plastid genome evolution within order- or family-level clades. The Thalassiosirales is one of the more comprehensively studied orders in terms of both genetics and morphology. Seven complete diatom plastid genomes are reported here including four Thalassiosirales: <i>Thalassiosira weissflogii</i>, <i>Roundia cardiophora</i>, <i>Cyclotella</i> sp. WC03_2, <i>Cyclotella</i> sp. L04_2, and three additional non-Thalassiosirales species <i>Chaetoceros simplex</i>, <i>Cerataulina daemon</i>, and <i>Rhizosolenia imbricata</i>. The sizes of the seven genomes vary from 116,459 to 129,498 bp, and their genomes are compact and lack introns. The larger size of the plastid genomes of Thalassiosirales compared to other diatoms is due primarily to expansion of the inverted repeat. Gene content within Thalassiosirales is more conserved compared to other diatom lineages. Gene order within Thalassiosirales is highly conserved except for the extensive genome rearrangement in <i>Thalassiosira oceanica</i>. <i>Cyclotella nana</i>, <i>Thalassiosira weissflogii</i> and <i>Roundia cardiophora</i> share an identical gene order, which is inferred to be the ancestral order for the Thalassiosirales, differing from that of the other two <i>Cyclotella</i> species by a single inversion. The genes <i>ilvB</i> and <i>ilvH</i> are missing in all six diatom plastid genomes except for <i>Cerataulina daemon</i>, suggesting an independent gain of these genes in this species. The <i>acpP1</i> gene is missing in all Thalassiosirales, suggesting that its loss may be a synapomorphy for the order and this gene may have been functionally transferred to the nucleus. Three genes involved in photosynthesis, <i>psaE</i>, <i>psaI</i>, <i>psaM</i>, are missing in <i>Rhizosolenia imbricata,</i> which represents the first documented instance of the loss of photosynthetic genes in diatom plastid genomes.</p></div

Phylogeny of Thalassiosirales and other diatom species based on twenty plastid protein-coding genes with gene/intron loss and plastid genome rearrangement events mapped on the branches.

<p>Number of genome inversions within Thalassiosirales were estimated based on Thalassiosirales ancestral genome using GRIMM <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107854#pone.0107854-Tesler1" target="_blank">[29]</a>. Taxa in bold are new genomes sequenced in this study.</p

Plastid genome maps of seven newly sequenced diatom species.

<p>Species that share the same circular map have the same gene order. Genes on the outside are transcribed clockwise; those on the inside counterclockwise. The ring of bar graphs on the inner circle display GC content in dark grey.</p

Comparison of inverted repeat boundaries in the seven diatom species newly sequenced for this study plus the two previously sequenced Thalassiosirales.

<p>Tree is that of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107854#pone-0107854-g002" target="_blank">Figure 2</a> with previously sequenced outgroup taxa pruned for visual simplicity. The numbers in brown indicate plastid genome size; the numbers in black below each genome fragment indicate the sizes of the LSC, IR and SSC, respectively. Protein coding genes at the IR boundaries are listed in blue. Three red gene blocks are <i>rrn5</i>, <i>rns</i> and <i>rnl</i>, respectively. Names in bold are Thalassiosirales. Underscored names are for taxa newly sequenced for this study.</p

Gene order comparison of the plastid genomes of seven diatoms sequenced for this study plus previously sequenced Thalassiosirales.

<p>Alignments were performed in Geneious R6 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107854#pone.0107854-Drummond1" target="_blank">[24]</a>with mauveAligner <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107854#pone.0107854-Darling1" target="_blank">[28]</a>. Taxon names in bold are members of the Thalassiosirales. Names underscored are those sequenced for this study.</p

Appendix 15 all-users-results

line Appendix 15. Combined results for all users. Details for Figure 3

Appendix 10 Diatoms-user-results

Online Appendix 10. Diatom user score

Appendix 12 Lilies-user-results

Online Appendix 12. Lilies user scores

Appendix 20 Instructions to Crowd

Online Appendix 20. Instruction sheets for the study participants (undergraduate students at Ohio State University)