Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Kuzmin, Dmitry A.; Feranchuk, Sergey; Sharov, Vadim V.; Cybin, Alexander N.; Makolov, Stepan V.; Putintseva, Yuliya A.; Орешкова, Н. В.; Krutovsky, Konstantin V.

doi:10.1186/s12859-018-2570-y

Cited by 44 publications

(50 citation statements)

References 33 publications

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“…menziesii (Mirb.) Franco) [38], and Siberian larch (Larix sibirica Ledeb) [39] have had their giga-genomes sequenced. These genome sequences offer an opportunity to identify millions of qualified SNPs through resequencing projects, and recently this has been initiated in loblolly pine by resequencing 10 different individual genomes [40].…”

Section: Discussionmentioning

confidence: 99%

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Zheng

Wei

et al. 2019

Forests

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Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low F ST (0.0285-0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies. breeder to address the population genetic architecture (genetic structure, diversity and relationship, etc.) and facilitate the accurate mating designs with parental analysis to accelerate the breeding progress [8]. The accessible molecular marker includes: (1) hybridization-based type such as restriction fragment length polymorphism (RFLP) and its modified forms, (2) PCR and electrophoresis-based type including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), inter simple sequence repeat (ISSR), and simple sequence repeat (SSR) etc., and (3) sequencing-based type dominated by single nucleotide polymorphism (SNP) [9][10][11]. Of these, SNPs have proved to be the most abundant form of variation within a species at genome level that provides more detailed insights into the genetic base of a population [10]. They have become more and more popular because they can be high-throughput detected through next-generation sequencing (NGS) at a moderate cost. Notably, the NGS-based SNP genoty...

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Section: Discussionmentioning

confidence: 99%

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Zheng

Wei

et al. 2019

Forests

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“…We used the Trinity software program to de novo assemble the high-quality sequencing data [19], which produced 120,951 transcripts with an N50 length of 1,467 bp and a mean length of 871 bp. The length distribution of the transcripts is shown in Supplemental Figure S1A and Table S2.…”

Section: Rna-seq and Transcriptome Assemblymentioning

confidence: 99%

“…Recent studies have shown that RNA-Seq is a very effective and powerful technique for gathering extensive transcriptome information in many plants [5][6][7][8]. When compared with other hardwood species [9][10][11][12][13][14][15], conifers tend to have larger and highly repetitive genomes [16][17][18][19][20][21]. Sequencing the P. neoveitchii genome remains expensive, even when using highthroughput Illumina sequencing technology.…”

Section: Introductionmentioning

confidence: 99%

The first transcriptome sequencing and analysis of the endangered plant species Picea neoveitchii Mast. and potential EST-SSR markers development

Pan

Zhu

Zhao

et al. 2019

Biotechnology & Biotechnological Equipment

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Picea neoveitchii Mast. is a rare and endangered evergreen coniferous tree species in China. P. neoveitchii grows within a specific ecological and geographical range. Here, we performed transcriptome sequencing of P. neoveitchii using the Illumina high-throughput deep sequencing technology with the following aims: (i) to perform de novo transcriptome assembly, (ii) to perform transcriptome assembly with functional annotation, (iii) to study the candidate genes involved in the biosynthesis of cellulose and lignin, (iv) to identify and analyse the transcription factors, and (v) to develop potential expressed sequence tag-simple sequence repeat (EST-SSR) markers for future population genomic and genome-wide association studies in P. neoveitchii. This is, to the best of our knowledge, the first study to provide a comprehensive transcriptome of P. neoveitchii. The transcriptome data contained 12.97 gigabase pairs (Gbp) for a total of 120,951 different transcripts belonging to 66,022 unigenes. In addition, we classified enzymes involved in the biosynthesis of cellulose and lignin and identified and analysed the transcription factors involved in stress responses, growth and development. Based on the larger than 1 kb unigenes, 1,814 EST-SSR markers were shown. Our results demonstrated that the transcriptome analysis is a valuable technology for non-model species with large genomes and this dataset will be an essential resource for future genetic and genomic research in P. neoveitchii.

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“…At the same time, it contained a very high fraction of contigs containing complete open reading frames, as revealed by the detection of 89.7% complete and just 4.1% fragmented tetrapod BUSCOs. Overall, the quality of the C. orientalis transcriptome, both in terms of number of orthologs present and in terms of complete BUSCOs identified, was significantly higher than most available amphibian reference transcriptomes 6,[21][22][23] . Completeness and fragmentation rates were comparable with the outcome of the most recent high-depth approaches targeting multiple tissues [24][25][26] (Fig.…”

Section: Resultsmentioning

confidence: 87%

“…These factors currently represent a significant challenge for whole genome assembly 5 , in particular due to the high computational resources required for handling the large amount of input sequencing data and the technical limitations of most assembly algorithms, optimized for genomes with a size comparable with human or smaller. The only exception was the axolotl genome (~32 Gb) 6 , which has been produced through a huge joint effort and at high costs, together with the development of ad hoc bioinformatics tools and computational strategies to manage the unusual size of the assembly.…”

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confidence: 99%

The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians

Biscotti

Carducci

Barucca

et al. 2020

Sci Rep

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Amphibians evolved in the Devonian period about 400 Mya and represent a transition step in tetrapod evolution. Among amphibians, high-throughput sequencing data are very limited for Caudata, due to their largest genome sizes among terrestrial vertebrates. in this paper we present the transcriptome from the fire bellied newt Cynops orientalis. Data here presented display a high level of completeness, comparable to the fully sequenced genomes available from other amphibians. Moreover, this work focused on genes involved in gametogenesis and sexual development. Surprisingly, the gsdf gene was identified for the first time in a tetrapod species, so far known only from bony fish and basal sarcopterygians. our analysis failed to isolate fgf24 and foxl3, supporting the possible loss of both genes in the common ancestor of Rhipidistians. in Cynops, the expression analysis of genes described to be sex-related in vertebrates singled out an expected functional role for some genes, while others displayed an unforeseen behavior, confirming the high variability of the sex-related pathway in vertebrates. Amphibians represent a group of vertebrates containing over 7,100 species worldwide 1. These organisms evolved in the Devonian period about 400 Mya and represent a transition step in tetrapod evolution 2. Modern-day amphibians have diverged into three orders with distinct anatomical features: Gymnophiona (caecilians, limbless amphibians), Caudata (salamanders and tritons), and Anura (frogs and toads). Amphibians have many features that make them ideal as animal models because of their physiology, diversity, phylogeny, and amazing capability of tissue regeneration. On the other hand, amphibians represent a case of global biodiversity crisis since they are among the most threatened species in the world 3. The Chinese fire-bellied newt, Cynops orientalis (David, 1873), is a small (6-10.3 cm long) urodele (Salamandridae: Pleurodelinae) distributed in Asia. It shows a color ranging from dark brown to black on the back and with belly from orange to scarlet red with numerous black spots. The sexual dimorphism is evident in size (males are smaller than females) and shape of tail and cloaca. C. orientalis lives in ponds and marshes and prefers cold and calm waters with a bottom of mud. In nature, in the Chinese region of Changsha, the reproduction period spans from March to July, when water temperatures range from 15 to 23 °C, and juveniles reach sexual maturity from 1 to 3 years. Data obtained by whole genome sequencing (WGS) are a very valuable resource to understand the evolutionary history and biology of species. Despite the importance of amphibians, the genomes of only 13 species have

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Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Cited by 44 publications

References 33 publications

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

The first transcriptome sequencing and analysis of the endangered plant species Picea neoveitchii Mast. and potential EST-SSR markers development

The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians

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