Sequencing of plant genomes ? a review

The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called 1396984945next-generation1396986481 sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics approaches have led to overcome the challenges that arose mainly in plant genomes with large size, high CG content, heterozygosity, transposable elements, repetitive DNA, and homopolymers or polyploidy, as may be the case with the most important crops. There is no doubt that the rest of the species will also benefit from such breakthroughs, which also include direct RNA sequencing without requiring cDNA synthesis. In fact, we are not in a postgenomic era as is sometimes stated, but rather in the beginning of a genomic revolution.

Sequencing of plant genomes ? a review

The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called 1396984945next-generation1396986481 sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics approaches have led to overcome the challenges that arose mainly in plant genomes with large size, high CG content, heterozygosity, transposable elements, repetitive DNA, and homopolymers or polyploidy, as may be the case with the most important crops. There is no doubt that the rest of the species will also benefit from such breakthroughs, which also include direct RNA sequencing without requiring cDNA synthesis. In fact, we are not in a postgenomic era as is sometimes stated, but rather in the beginning of a genomic revolution.

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Turkish Journal of Agriculture and Forestry-Cover
  • ISSN: 1300-011X
  • Yayın Aralığı: Yılda 6 Sayı
  • Yayıncı: TÜBİTAK
Sayıdaki Diğer Makaleler

Preface - Special Issue on: 'Genomics and transcriptomics for utilization of plant genetic resources and crop improvement'

Turgay ÜNVER, Gabriel DORADO, Baohong ZHANG

Sequencing of plant genomes ? a review

Mine TÜRKTAŞ, Kuaybe Yücebilgili KURTOĞLU, Gabriel DORADO, Baohong ZHANG, Pilar HERNANDEZ, Turgay ÜNVER

Molecular cloning of BnZEP and its expression in petals of different colors inBrassica napus L.

JUN JIANG, LUSHEN TIAN, SHIXING GUO, QINGQING YU, Dezhi ZENG, YINGZE NIU

Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana

RAJINDER KAUR, NEHA SHARMA, RAVINDER RAINA

Identification of expressed resistance gene analog sequences in coconut leaf transcriptome and their evolutionary analysis

Muliyar Krishna RAJESH, Kaitheri Edathil RACHANA, Sudalaimuthu Asari NAGANEESWARAN, Rahman SHAFEEQ, Regi Jacob THOMAS, Mohammed SHAREEFA, Babu MERIN, Karun ANITHA

Genetic variability, heritability, and genetic advance in strawberry(Fragaria × ananassa Duch.)

PRANAV KUMAR MISHRA, RAM BADAN RAM, NEERAJ KUMAR

Cytoplasmic-nuclear variation in a diversity-fixed foundation set ofBrassica juncea (L.) Czern & Coss.

JAVED AKHATAR, NITIN KUMAR, CHHAYA ATRI, SURINDER SINGH BANGA

Transcriptome characterization and large-scale identification of SSR/SNPmarkers in symbiotic nitrogen fixation crop faba bean (Vicia faba L.)

SUNDAN SURESH, TAE-SUNG KIM, SEBASTIN RAVEENDAR, JOON-HYEONG CHO, JUNG YOON YI, MYUNG CHUL LEE, SOK-YOUNG LEE, HYUNG-JIN BAEK, GYU-TAEK CHO, JONG WOOK CHUNG

Generation of transgenic sugar beet (Beta vulgarism L.) overexpressing the polygalacturonase inhibiting protein 1 of Phaseolus vulgaris (PvPGIP1) through Agrobacterium-mediated transformation

REZA MOHAMMADZADEH, MOSTAFA MOTALLEBI, MOHAMADREZA ZAMANI, ZAHRA MOGHADDASSI JAHROMI, PEYMAN NOROUZI, MANUEL BENEDETTI, GIULIA DE LORENZO

Physiological characteristics, antioxidant enzyme activities, and gene expression in 2 spring canola (Brassica napus L.) cultivars under drought stress conditions

SEYED MOHAMMAD HOSSEINI, TAHEREH HASANLOO, SAEED MOHAMMADI