Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions

<p>Abstract</p> <p>Background</p> <p>Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to draw a transcriptomic atlas of <it>Oryza sativa japonica </it>(rice) mitochondria, which was predicted to be approximately 490-kb long.</p> <p>Results</p> <p>Whereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of RNA expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. The newly identified open reading frames (ORFs) predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these ORFs did not play a role in mitochondrial principal functions. We also identified two partial fragments of retrotransposon sequences as being transcribed in rice mitochondria.</p> <p>Conclusion</p> <p>The present study indicated the previously unexpected complexity of plant mitochondrial RNA metabolism. Our transcriptomic data (<it>Oryza sativa </it>Mitochondrial rna Expression Server: OsMES) is publicly accessible at [<url>http://bioinf.mind.meiji.ac.jp/cgi-bin/gbrowse/OsMes/#search</url>].</p

Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes

ウミヘビ類のゲノム解読に成功 --海洋環境への適応進化の分子的基盤を探る--. 京都大学プレスリリース. 2019-09-11.Marine amniotes, a polyphyletic group, provide an excellent opportunity for studying convergent evolution. Their sense of smell tends to degenerate, but this process has not been explored by comparing fully aquatic species with their amphibious relatives in an evolutionary context. Here, we sequenced the genomes of fully aquatic and amphibious sea snakes and identified repertoires of chemosensory receptor genes involved in olfaction. Snakes possess large numbers of the olfactory receptor (OR) genes and the type-2 vomeronasal receptor (V2R) genes, and expression profiling in the olfactory tissues suggests that snakes use the ORs in the main olfactory system (MOS) and the V2Rs in the vomeronasal system (VNS). The number of OR genes has decreased in sea snakes, and fully aquatic species lost MOS which is responsible for detecting airborne odours. By contrast, sea snakes including fully aquatic species retain a number of V2R genes and a well-developed VNS for smelling underwater. This study suggests that the sense of smell also degenerated in sea snakes, particularly in fully aquatic species, but their residual olfactory capability is distinct from that of other fully aquatic amniotes. Amphibious species show an intermediate status between terrestrial and fully aquatic snakes, implying their importance in understanding the process of aquatic adaptation

Supplemental Data S1

Deduced amino acid sequences of the intact GPCR genes identified in this study

Supplemental Table S9

Locus of each gene of Laticauda colubrina identified in this study

Supplemental Table S12

Locus of each gene of a common viper (Vber1.0, GenBank accession GCA_000800605.1) identified in this study

Supplemental Table S7

Locus of each gene of Emydocephalus ijimae identified in this study

Supplemental Table S6

Locus of each gene of Hydrophis melanocephalus identified in this study

Supplemental Table S13

Locus of each gene of a green anole (AnoCar2.0, GenBank accession GCA_000090745.2) identified in this study