Daily Archives: November 26, 2014

As one of the most diverse plant family, orchid now has its first genome sequenced and the result is published at Nature Genetics as a cover article.

This study is an accomplishment of the Orchid Genome Project, an international collaboration led by Lai-Qiang Huang and Zhong-Jian Liu at Tsinghua University and National Orchid Conservation Center in Shenzhen China, with colleagues from different institutions, including Chengkong University in Taiwan, Ghent University in Belgium, and Institute of Botany of CAS in Beijing.

The team carried out whole genome sequencing on phalaenopsis equestris, which is an important parental species for breeding of commercial phalaenopsis strains. P. equestris is also the first plant with Crassulacean Acid Metabolism (CAM) for which the genome has been sequenced. The assembled genome contains 29,431 predicted protein-coding genes. The average intron length is 2,922 base pairs, which is much longer than in any sequenced plant genomes. Further analysis indicate that transposable elements in introns are the major reason why orchid genes have so big introns.

As heterozygosity post great challenge for whole genome sequencing and assembly, the orchid genome is by no means an exception. In the orchid genome, they found that contigs likely to be under-assembled owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. Those genes could be candidates for further research on the mechanism of self-incompatibility in orchid.

As in many plant genomes, they also found evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades. This is possibly an important clue to why orchid developed into one of the largest plant families on earth.

By comparing with homolog genes in other plant genomes, they found gene duplication and loss in CAM genes along the lineage to orchid. This result suggests that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris.

Finally, they found expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

All around the world, orchids are highly endangered species because of illegal collection and habitat loss. The complete genome sequence of P. equestris will provide an important resource to explore orchid diversity and evolution at the genome level. The genome sequence will also be a key resource for the development of new concepts and techniques in genetic engineering, such as molecular marker-assisted breeding and the production of transgenic plants, which are necessary to increase the efficiency of orchid breeding and aid orchid horticulture research.

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Scientists completed the first orchid whole genome sequencing

Researchers in human genetics have known that long nucleotide repeats in DNA lead to instability of the genome and ultimately to human hereditary diseases such Freidreich's ataxia and Huntington's disease.

Scientists have believed that the lengthening of those repeats occur during DNA replication when cells divide or when the cellular DNA repair machinery gets activated. Recently, however, it became apparent that yet another process called transcription, which is copying the information from DNA into RNA, could also been involved.

A Tufts University study published online on November 20 in the journal Cell Reports by a research team lead by Sergei Mirkin, the White Family Professor of Biology at Tufts' School of Arts and Sciences, along with former graduate student Kartick Shah and graduate students Ryan McGuity and Vera Egorova, explores the relationship between transcription and the expansions of DNA repeats. It concludes that the active transcriptional state of a DNA segment containing a DNA repeat predisposes it for expansions. The print version of the study will be published on December 11.

"There are a great many simple repetitive motifs in our DNA, such as GAAGAAGAA or CGGCGGCGG," says Mirkin. "They are stable and cause no harm if they stay short. Occasionally, however, they start lengthening compulsively, and these uncontrollable expansions lead to dramatic changes in genome stability, gene expression, which can lead to human disease."

In their study, the researchers used baker's yeast to monitor the progress and the fundamental genetic machineries for transcription, replication and repair in genome functioning.

"The beauty of the yeast system is that it provides one with a practically unlimited arsenal of tools to study the mechanisms of genome functioning," says Mirkin. "We created genetic systems to track down expansions of the repeats that were positioned in either transcribed or non-transcribed parts of reporter genes."

After measuring the rate of repeat expansions in all these cases, the authors found that a repeat can expand under the condition when there is practically no transcription, but the likelihood of the expansion process is drastically (10-fold) higher when the reporter is transcriptionally active.

Surprisingly, however, transcription machinery does not need to physically pass through the repeat to stimulate its expansion. Thus, it is the active transcription state of the repeat-containing DNA segment, rather than RNA synthesis through the repeat that promotes expansions.

In the transcriptionally active state, DNA is packaged in chromatin more loosely than when it is transcriptionally inactive. More specifically, the density of nucleosomes along the transcribed DNA segment is significantly lower than that in the non-transcribed segment. This packaging of repetitive DNA within the transcribed areas gives much more room for DNA strand gymnastics, ultimately leading to repeat expansions.

Whatever the exact model, says Mirkin, the fact that expandable DNA repeats were always found in transcribed areas of our genome may not be that surprising after all.

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Link between DNA transcription, disease-causing expansions