Wang, C.-S. | bioRxiv Science

bioRxiv2026

Assembling and annotating the Tainung 67 rice genome to trace its japonica and indica ancestries

Here we reported the 409.0 Mb assembly of the Tainung 67 (TNG67) genome, an early hybrid of japonica and indica cultivars. We used different platforms to sequence the TNG67 genome with a total coverage of 209.8x, from a combination of Illumina paired-end reads, Illumina mate-pair reads, and Oxford Nanopore Technology long reads. The assembly has an N50 of 32.3 Mb with the longest scaffold = 45.2 Mb. We have annotated 38,938 genes where 28,376 (72.9%) finished with the Blast2GO annotation stage. There were 4,821 genes, (98.4%) of the total gene count that have complete BUSCOs. 48.33% (197.5Mb) of the TNG67 genome is composed of repeats. We predicted a total of 527 blast-resistant genes in TNG67. We also analyzed a total of 20 grain size genes and 38 photoperiod-related genes of TNG67, Nipponbare and TN1, and grouped them in terms of whether the TNG67 genes are more similar to Nipponbare, more similar to TN1, hybrid, same, or unique. We also determined whether the sequences of the TNG67 genome were derived from its japonica or indica ancestors. This TNG67 genome may help rice researchers improve yield, develop resistance against biotic and abiotic stress, and understand the evolution of a hybrid cultivar of japonica and indica.

genomics↗

bioRxiv2021

Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution

BackgroundTaichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. ResultsAligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. ConclusionsWe have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1s blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.

genomics↗

bioRxiv2020

Two-photon microscopy at >500 volumes/second

We demonstrate a multi-focal multi-photon volumetric microscopy via combination of 32-beam parallel lateral-scanning, a 70-kHz axial-scanning acoustic lens, and a 32-channel photodetector, enabling unprecedented data rate (2-10 GHz) and >500-volumes/second imaging speed over ~200x200x200-m3.

biophysics↗