Draft genome sequence of the rubber tree Hevea brasiliensis

Rahman, Azimah Abd; Usharraj, Abhilash O; Misra, Biswapriya B.; Thottathil, Gincy P.; Jayasekaran, Kandakumar; Feng, Yun; Hou, Shaobin; Ong, Su Yean; Ng, Fui Ling; Lee, Ling Sze; Tan, Hock Siew; Sakaff, Muhd Khairul Luqman Muhd; Teh, Beng Soon; Khoo, Bee Feong; Badai, Siti Suriawati; Aziz, Nurohaida Ab; Yuryev, Anton; Knudsen, Bjarne; Dionne‐Laporte, Alexandre; Mchunu, Nokuthula Peace; Yu, Qingyi; Langston, Brennick J.; Freitas, Tracey; Young, Aaron G.; Chen, Rui; Wang, Lei; Najimudin, Nazalan; Saito, Jennifer A.; Alam, Maqsudul

doi:10.1186/1471-2164-14-75

Cited by 238 publications

(231 citation statements)

References 85 publications

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“…Constrained portions of the cassava genome were identified by quantifying rejected substitutions (strength of purifying selection) with the GERP++ program 16 . Multiple whole-genome sequence alignment was carried out for the seven species in the Malpighiales clade of the plant kingdom, including cassava, rubber (H. brasiliensis) 39 , jatropha (Jatropha curcas) 40 , castor bean (Ricinus communis) 41 , willow (Salix purpurea) 42 , flax (Linum usitatissimum) 43 , and poplar (Populus trichocarpa) 44 . Whole-genome alignment was carried out with the Large-Scale Genome Alignment Tool (LASTZ) 45 .…”

Section: Alignment Of Reads and Variant Calling Of Cassava Haplotypementioning

confidence: 99%

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

et al. 2017

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Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these deleterious mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions and identified >28 million segregating variants. We found that (i) although domestication has modified starch and ketone metabolism pathways to allow for human consumption, the concomitant bottleneck and clonal propagation have resulted in a large proportion of fixed deleterious amino acid changes, increased the number of deleterious alleles by 26%, and shifted the mutational burden toward common variants; (ii) deleterious mutations have been ineffectively purged, owing to limited recombination in the cassava genome; (iii) recent breeding efforts have maintained yield by masking the most damaging recessive mutations in the heterozygous state but have been unable to purge the mutation burden; such purging should be a key target in future cassava breeding.For millions of people in the tropics, cassava is the third most consumed carbohydrate source, after rice and maize 1 . Even though cassava was domesticated in Latin America 2,3 , it has spread widely and has become a major staple crop in Africa. Although its wild progenitor, M. esculenta sp. falbellifolia, reproduces by seed 4 , cultivated cassava is notably almost exclusively clonally propagated via stem cutting 5 . The limited number of recombination events in such vegetatively propagated crops may result in an accumulation of deleterious alleles throughout the genome 6 . Thus, mutation burden in cassava is expected to be more severe than that in sexually propagated species. Deleterious mutations are considered to be at the heart of inbreeding depression 7 . Even in elite cassava accessions, inbreeding depression is extremely severe, and a single generation of inbreeding may result in a >60% decrease in fresh root yield 8,9 . In this study, we sought to identify deleterious mutations in cassava populations, with the goal of accelerating cassava breeding by allowing breeders to purge deleterious mutations more efficiently.We conducted a comprehensive characterization of genetic variation by whole-genome sequencing (WGS) of 241 cassava accessions ( Fig. 1, Supplementary Fig. 1 and Supplementary Table 1). On average, more than 30× coverage was generated for each accession. To ensure high-quality variant discovery, variants from low-copynumber regions of the cassava genome 10,11 were identified to develop the cassava haplotype map II (HapMapII) (Supplementary Fig. 2), containing 25.9 million SNPs and 1.9 million insertions/deletions (indels) (Supplementary Table 2), of which nearly 50% were rare (minor-allele frequency <0.05) (Supplementary Fig. 3). The error rate of variant calling, i.e., the proportion of segregating sites in the reference accession, was 0.01%. The correlation between read depth and the proportion of SNP heterozygosity was extremely low (r 2 = 6 × 10...

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Section: Alignment Of Reads and Variant Calling Of Cassava Haplotypementioning

confidence: 99%

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

et al. 2017

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“…Oleh karena itu, pendekatan in silico melalui bioinformatika dapat digunakan untuk mempercepat analisis dalam prediksi famili gen PI (Penders et al, 2008). Selain itu, informasi genom karet dari klon RRIM 600 dan Reyan 7-33-97 telah tersedia dan dapat diakses secara daring pada basis data European Nucleotide Archive (ENA) (Lau et al, 2016;Rahman et al, 2013;Tang et al, 2016).…”

Section: Pendahuluanunclassified

Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome)

Martiansyah¹,

Putranto²,

Khumaida³

2017

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Protease inhibitors (PIs) are small proteins that form complexes with proteases and inhibits their proteolytic activity. Its potential application as an antimicrobial agent has been studied. Most of PIs' molecule size is around 8-22 kDa depending on their protein families.To date, on the basis of sequence homologies of inhibitor domains, PIs have been classified into 48 families in all organisms. In plant, more than 13 families of PIs have been identified but they were not widely identified in the rubber tree (Hevea brasiliensis Muell.Arg). In the present study, 40 putative HbPI genes, designated as HbPI01 to HbPI36, were identified from whole-genome sequence of rubber tree clone Reyan 7-33-97 using 7453 scaffolds available online in NCBI with the accession code: LVXX01000000. Multiple sequence alignment using MUSCLE algorithm discovered seven conserved motifs (Motifs I-VII) among HbPIs. Phylogenetic analysis of 50 and 36 PI amino acid residues of 32 scaffolds containing putative PI genes from Arabidopsis thaliana and H. brasiliensis showed three clusters (families): LTP-I, SERPIN and LTP-II. LTP-I has 23 putative HbPI genes (HbPI05 to HbPI27) and 12 AtPI genes. SERPIN, a family member of serine protease inhibitor group, has 11 putative HbPI genes (HbPI01 to HbPI04 and HbPI28 to HbPI34) and 22 AtPI genes. LTP-II has 2 putative HbPI genes (HbPI35 to HbPI36) and 16 AtPI genes. In conclusion, this work provides valuable information for further functional characterization of HbPI genes in H. brasiliensis.[Key words: protease inhibitor, genome-wide, scaffold, in silico, Hevea brasiliensis]. AbstrakProtease inhibitor (PI) merupakan protein yang membentuk kompleks dengan protease dan menghambat aktivitas proteolitik dari enzim tersebut. Potensi penggunaan protease inhibitor sebagai agensia antimikroba telah diketahui. Kebanyakan PI memiliki ukuran molekul sekitar 8-22 kDa bergantung pada familinya. Saat ini, PI dapat diklasifikasikan menjadi 48 famili di seluruh organisme berdasarkan kemiripan sekuen dari domain inhibitornya. Pada tanaman, lebih dari 13 famili PI telah diketahui tetapi pada tanaman karet (Hevea brasiliensis Muell.Arg) belum diidentifikasi. Pada penelitian ini, sebanyak 40 gen putatif penyandi PI (HbPI01 hingga HbPI36) telah berhasil diidentifikasi dari 7453 scaffold genom utuh tanaman karet klon Reyan 7-33-97 yang tersedia secara daring dengan kode aksesi LVXX01000000. Penjajaran sekuen menggunakan algoritma MUSCLE memper-lihatkan tujuh konservasi motif (Motif I-VIII) pada famili gen putatif HbPIs. Analisis pohon filogenetik dari tanaman Arabidopsis thaliana dan H. brasiliensis sebanyak 50 dan 36 sekuen residu asam amino dari 32 scaffold yang mengandung gen putatif PI menunjukkan adanya tiga klaster besar, yaitu famili LTP-I, SERPIN dan LTP-II. LTP-I terdiri dari 23 gen putatif HbPI (HbPI05 hingga HbPI27) dan 12 gen AtPI. SERPIN yang merupakan anggota kelas protease inhibitor serin terdiri dari 11 gen putatif HbPI (HbPI01hingga HbPI04 dan HbPI28 hingga HbPI34) dan 22 gen AtPI. LTP-II terdiri dari 2 gen putatif HbPI (HbPI35 hingga HbPI36) dan 16 gen AtPIs. Penelitian ini menghasilkan informasi penting untuk melakukan karakterisasi fungsional lebih mendalam pada gen HbPI tanaman karet ke depannya.[Kata kunci: protease inhibitor, genome-wide,scaffold, in silico, Hevea brasiliensis].

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“…Teknik rekayasa genetika pada tanaman karet semakin lebih mudah dilakukan dengan telah berhasil disusunnya konsep genom (Rahman et al, 2013) dan pustaka cDNA dari lateks (Han et al, 2000;Chotigeat et al, 2010). Hasil penelitian tersebut menunjukkan jumlah gen diperkirakan sebesar 68.955 gen, dan 12,7 % dari jumlah gen tersebut merupakan gen unik pada Hevea.…”

Section: Rekayasa Genetikaunclassified

“…Hasil penelitian tersebut menunjukkan jumlah gen diperkirakan sebesar 68.955 gen, dan 12,7 % dari jumlah gen tersebut merupakan gen unik pada Hevea. Gen-gen tersebut berhubungan d e n g a n b i o s i n t e s i s p a r t i k e l k a r e t , pembentukan kayu, resistensi penyakit dan proses alergenisitas (Rahman et al, 2013). Perkembangan penelitian menggunakan teknik rekayasa genetika pada tanaman karet masih terbilang baru dibandingkan dengan tanaman lain karena memiliki banyak faktor pembatas.…”

Section: Rekayasa Genetikaunclassified

UPAYA PERBAIKAN GENETIK DAN PENYEDIAAN BIBIT TANAMAN KARET (Hevea brasiliensis Muell. Arg.) MELALUI PENDEKATAN BIOTEKNOLOGI

Darojat¹,

Tistama²

2014

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AbstrakBeberapa tantangan dalam kegiatan perakitan klon unggul baru tanaman karet (Hevea brasiliensis Muell. Arg.) melalui metode p e r s i l a n g a n b u a t a n ( k o nve n s i o n a l ) diantaranya adalah membutuhkan waktu yang lama, sifat heterozigositas yang tinggi dan tingkat keberhasilan yang belum optimal. Bioteknologi diharapkan dapat menjadi metode pendukung dalam menjawab t a n t a n g a n y a n g t e r j a d i t e r s e b u t . Perkembangan teknik in vitro dan rekayasa genetika telah memberikan terobosan baru dalam perbanyakan dan perbaikan genetik tanaman karet. Pemanfaatan bioteknologi telah berdampak pada proses perbaikan g e n e t i k t a n a m a n k a r e t d a l a m h a l produktivitas, kesehatan tanaman, dan peningkatan toleransi terhadap cekaman. Selain itu penggunaan marka molekuler sangat bermanfaat untuk percepatan seleksi dalam kegiatan pemuliaan tanaman karet. Teknik tersebut juga berguna dalam identifikasi klon dan tetua, analisis keanekaragaman genetik, pengawasan hasil persilangan buatan, penciri klon dan biologi reproduksi. Tulisan ini menjabarkan tentang pendekatan bioteknologi untuk meningkatkan potensi genetik tanaman karet.

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Draft genome sequence of the rubber tree Hevea brasiliensis

Cited by 238 publications

References 85 publications

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome)

UPAYA PERBAIKAN GENETIK DAN PENYEDIAAN BIBIT TANAMAN KARET (Hevea brasiliensis Muell. Arg.) MELALUI PENDEKATAN BIOTEKNOLOGI

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