Wet=experimental biology. Dry=computational informatics.

Importance of bioinformatics has long been mentioned in plant genomics field. However, not many labs successfully establish working environment that enhance the synergism between wet and dry. Our lab is trying to make a lab environment that facilitate members to get familiar with both fields.

Plant is able to establish physical link between individuals. Taking this advantage, is it possible to obtain information and materials produced by plant without cutting down plant body, alternatively, by transporting through pipeline that interconnects plant individuals?

  It is often seen that many shoots of mint or bamboo are connected by underground stem. However, this is an example of non-sexual proliferation, rather than interconnection. Example of connection of plant individuals is seen in the cases of parasitic and symbiotic plants.

   In our lab, we are interested in the molecular mechanisms underlying the establishment of vascular connection between parasitic plant and its host plant. We are also interested in applying the mechanism of the vascular connection to development of plant's novel function as "green pipeline" to transport information and metabolites long distance. At the same time, by using the knowledge on parasitism establishment, we are interested in developing a novel method to control parasitic plants that threaten crop production.

Parasitic events between Orobanche and tomato root
Parasitic events between Orobanche and tomato root
Steps toward green pipeline
Steps toward green pipeline

Our reserach is on Information science.

But I do not mean we are doing the Bioinformatics.

We are interested in the way how plants generate and translate information.

 

Our problems:

How plants choose pieces of information they need?

How plants translate information input into cellular output?

How individual plant transmits information to other individual plant?

 


Micro-Tom genome

We read whole genome sequence of the model tomato cultivar Micro-Tom with financial support from MEXT NBRP genome information upgrading program in 2010. By using HiSeq2000 and 454 GS-FLX, we obtained reads with 144-fold coverage of the tomato genome (0.9 Gb). Comparison of Micro-Tom genome sequence with the tomato reference genome sequence of Heinz 1706 revealed that there are approximately 1.2 M SNPs and 0.19 M Indels between two cultivars.

  To further analyze intraspecific differences, we are focusing on

(1)annotation of SNPs and Indels.

(2)whether distribution of SNPs/Indels depends on gene family.

(3)combining results of deep CAGE and RNAseq.

(4)mapping Micro-Tom BAC end-sequences.

(5)constructing Genome Browser.

 


Micro-Tom Transcription Start Site (TSS) profiling

When we analyzed full-length cDNAs of Micro-Tom, we found that heterogeneity of 5'-end occured in transcripts from a large number of genes. This implies that transcription start site changed according to the organs, or according to the fruit developmental stage.

  This motivated us to perform TSS profiling of three developmental stages of Micro-Tom fruit (immature green, mature green, and red) using DeepCAGE method. We are further planning to perform TSS profiling of different tomato tissues including epidermis and locular tissues.

Transcription Start Site determination using DeepCAGE
Transcription Start Site determination using DeepCAGE

Transcripts Containing Retained Introns

From the comprehensive analysis of Micro-Tom full-length cDNAs, we found that approximately 6 % of the transcripts have retained introns. What is biological role of the intron-containing transcripts? First, it naturaly produce proteins from a gene with different amino acid seqiences. Alternatively, it may play a role in producing siRNA from repeat-rich retained intron.

 To clarify the biological role of the retained-intron transcripts, we are trying to analyze

1) a translatome profile obtained from purifyed ribosome-bound RNA

2) small RNAs that match retained intron sequence.

Alternative splicing transcripts found in Micro-Tom full-length cDNA collection.
Alternative splicing transcripts found in Micro-Tom full-length cDNA collection.

Learn how to connect vascular tissues from the root parositic plant Orobanche