【免费】decodingthemassiveloblollypinegenome资源-CSDN文库

需积分: 0 141 浏览量 2015-02-03 10:37:17 上传评论收藏 1.98MB PDF 举报

### 解码大容量长叶松基因组 #### 背景与挑战本文介绍了一项重大的科研成就：成功解码了长叶松（Pinus taeda L.）的庞大基因组。在此之前，针叶树类（如松树）的基因组大小及其复杂性一直是阻碍全基因组测序及组装的主要障碍。长叶松作为一种经济价值高且具有广泛研究基础的物种，自然成为了早期全基因组测序尝试的理想候选者。 #### 测序策略为了克服上述挑战，研究团队采用了一种创新策略来完成长叶松基因组的测序工作。该方法结合了长叶松独特的生殖生物学特征与先进的基因组组装技术。具体而言，研究者利用了来自单个长叶松个体（编号为20-1010）的单倍体种子胚乳作为测序材料。该样本来源于工业林木育种项目，因此其遗传背景相对稳定，有助于提高测序数据的质量和连贯性。 #### 测序技术与数据处理在测序过程中，主要采用了新一代测序技术（Next-Generation Sequencing, NGS），特别是针对单个单倍体种子胚乳的全基因组鸟枪法测序。这种技术能够高效地生成大量短序列片段，随后通过算法组装成更长的连续序列。此外，为了确保数据质量，研究人员还对测序数据进行了严格的质量控制和过滤。 #### 基因组组装与特征通过对上述测序数据进行处理和组装，研究团队构建了一个初步的基因组草图，覆盖长度达到了23.2 Gbp（十亿碱基对），其中20.1 Gbp被有效组装，N50 scaffold大小为66.9 kbp。这一成果显著提高了针叶树类基因组的组装水平。更重要的是，该基因组的长scaffold长度使得研究者能够注释出50,172个基因模型，其中内含子平均长度超过2.7 kbp，有些甚至超过了100 kbp。 #### 重复序列分析除了基因注释之外，研究团队还对长叶松基因组中的重复序列进行了深入分析。重复序列通常占植物基因组的很大比例，并对基因组结构和功能有重要影响。根据对重复序列的denovo分析，估计它们占据了长叶松基因组的大约82%，并据此更新和扩展了现有的重复序列库。 #### 同源基因家族鉴定通过对同源基因集的分析，研究者发现了一些可能仅存在于针叶树中的基因家族。这些基因家族可能与针叶树特有的生物学特性或适应环境的能力有关，为进一步探索针叶树的进化历程提供了重要线索。 #### 结论与展望长叶松基因组的成功解码不仅为研究人员和育种者提供了一个宝贵的资源库，也为未来其他大型复杂基因组的研究开辟了新途径。该研究展示了一种创新的测序策略，有望应用于更多具有巨大基因组的生物种类，从而促进整个生命科学领域的发展。此外，这项工作还强调了跨学科合作的重要性，尤其是在解决生物学难题时所展现出的强大潜力。

资源推荐

资源详情

资源评论

RES E AR C H Open Access

Decoding the massive genome of loblolly pine

using haploid DNA and novel assembly strategies

David B Neale

, Jill L Wegrzyn

, Kristian A Stevens

, Aleksey V Zimin

, Daniela Puiu

, Marc W Crepeau

Charis Cardeno

, Maxim Koriabine

, Ann E Holtz-Morris

, John D Liechty

, Pedro J Martínez-García

Hans A Vasquez-Gross

, Brian Y Lin

, Jacob J Zieve

, William M Dougherty

, Sara Fuentes-Soriano

, Le-Shin Wu

Don Gilbert

, Guillaume Marçais

, Michael Roberts

, Carson Holt

, Mark Yandell

, John M Davis

Katherine E Smith

, Jeffrey FD Dean

, W Walter Lorenz

, Ross W Whetten

, Ronald Sederoff

Nicholas Wheeler

, Patrick E McGuire

, Doreen Main

, Carol A Loopstra

, Keithanne Mockaitis

, Pieter J deJong

James A Yorke

, Steven L Salzberg

and Charles H Langley

Abstract

Background: The size and complexity of conifer genomes has, until now, prevented full genome sequencing and

assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early

candidate for reference sequence determination.

Results: We develop a novel strategy to sequence th e genome of loblolly pine that combines unique aspects

of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach

relying primarily on next generation sequence generated from a single haploid seed megagametophyte from

a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and

assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold

size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths

allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding

100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We

further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content,

estimated to encompass 82% of the genome.

Conclusions: In addition to its value as a resource for researchers and breeders, the loblolly pine genome

sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex

genomes of this important group of plants that can now be widely applied.

Background

Advances in sequencing and assembly technologies have

made it possible to obtain reference genome sequences

for organisms once thought intractable, including the

leviathan genomes (20 to 40 Gb) of conifers. Gymno-

sperms, represented principally by a diverse and majestic

array of conifer species (approximately 630 species, dis-

tributed across eight families and 70 genera [1]), are one

of the oldest of the major plant clades, having arisen

from ancestral seed plants some 300 million years ago.

Conifers will likely provide many genome-level insights

on the origins of genetic diversity in higher plants.

Though today’s conifers may be considered relics of a

once much-larger set of taxa that thrived throughout the

age of the dinosaurs (250 to 65 millions of years ago)

[2,3], they remain the dominant life forms in many of

the temperate and boreal ecosystems in the North ern

Hemisphere and extend into subtropical regions and the

Southern Hemisphere.

We chose to investigate the loblolly pine (Pinus taeda

L.) genome because of its well-d eveloped scientific re-

sources. Over 1.5 billion seedlings are planted annually,

approximately 80% of which are genetically improved,

* Correspondence: dbneale@ucdavis.edu

Department of Plant Sciences, University of California, Davis, CA, USA

Full list of author information is available at the end of the article

Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and

reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain

Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article,

unless otherwise stated.

Neale et al. Genome Biology 2014, 15:R59

http://genomebiology.com/2014/15/3/R59

driving its selection as the reference conifer genome.

Among conifers, its genetic resources are uns urpassed in

that three tree improvement coope ratives have been

breeding loblolly pine for more than 60 years and man-

age millions of trees in genetic trials. The current con-

sensus reference genetic map for loblolly pine is made

up of 2,308 genetic markers [4]. Extensive QTL and as-

sociation mapping studies in loblolly pine have revealed

a great deal about the genetic basis of complex traits

such as physical and chemical wood properties, disease

and insect resistance, growth, and adaptation to chan-

ging environments. Current research focuses on the

potential of genomic selection for continued genetic im-

provement [5].

The tree selected for sequencing, ‘20-1010’, is a mem-

ber of the North Carolina State University-Industry Co-

operative Tree Improvement Program and the property

of the Commonwealth of Virginia Department of For-

estry, which released this germplasm into the public

domain. In accordance with open access policies [6], we

released the first draft genome of loblolly pine in June

2012, which made it the first draft assembly available for

any gymnosperm. The draft described here represents a

significant advance over available gymnosperm reference

sequences [7,8].

Results and discussion

Sequencing and assembly

The loblolly pine genome [9] joins the two other conifer

reference sequences produced recently [7,8]. With an esti-

mated 22 billion base pairs [10], it is the largest genome

sequenced and assembled to date. Our experimental de-

sign leveraged a unique feature of the conifer life cycle

and new computational approaches to reduce the assem-

bly problem to a tractable scale [9,11]. From the first

whole genome shotgun (WGS) assembly of the 1.8 million

base pair Haemophilus influenzae genome in 1995 to the

orders-of-magnitude larger three-billion-base-pair mam-

malian genomes that followed years later [12], the WGS

protocol has been an efficient and effective method of pro-

ducing high quality reference genomes. This was in part

made possible by the overlap layout consensus (OLC) as-

sembly paradigm championed by Myers [13] and ubiqui-

tously implemented in first-generation WGS assemblers.

When next-generation sequencing disruptively ushered in

a new era of WGS sequencing, the extremely large num-

bers of reads exceeded the capabilities of existing OLC

assemblers. To circumvent this, new assemblers were de-

veloped, using short k-mer based methods first described

by Pevzner [14]. The giant panda [15] was the first mam-

malian species to have its genome produced using strictly

NGS reads. For loblolly pine, we utilized a hybrid assembly

method that incorporates both k-mer based and OLC as-

sembly methods.

Figure 1A illustrates the two sources of DNA that

comprised the sequencing strategy. As outlined below

(see [9] for details), the maj ority of the WGS sequence

data in Table 1 was generated from a single pine seed

megagametophyte. The small quantity of genomic DNA

obtained from the haploid megagametophyte tissue was

used to construct a series of 11 Illumina paired end li-

braries with sufficient complexity to form the basis of a

high quality WGS assembly. The use of haploid DNA

greatly simplifies assembly, but the limited quantity of

haploid DNA was insufficient for the entire project. Dip-

loid needle tissue served as an abundant source of par-

ental DNA for the construction of long-insert linking

libraries. This included 48 libraries ranging from 1 to 5.5

kilobase pairs (Kb) and nine fosmid DiTag libraries span-

ning 35 to 40 Kb.

An overview of the assembly process is presented in

Figure 1B. The combined 63× cover age from megagame-

tophyte libraries (approximately 15 billion reads) was

used for error correction and for the construction of a

database of 79-mers appearing in the haploid genome.

This database wa s used to filter highly divergent haplo-

types from the diploid sequence data. The super-read re-

duction implemented in the MaSuRCA assembler [11]

condensed most of the haploid paired-end reads into a

set of approximately 150 M longer ‘super-reads’. Each

super-read is a single contiguous haploid sequence that

contains both ends of one or more paired-end reads.

The construction process ensured that no super-read

was contained in another super-read. Critically, the

number of megagametophyte-derived reads was reduced

by a factor of 100. The combined dataset was 27-fold

smaller than the original, and was sufficie ntly reduced in

size to make overlap-based assembly using CABOG [16]

possible. The output of the MaSuRC A assembly pipeline

became assembly 1.0. Additional scaffolding methods

were implemented to improve the assembly by taking

advantage of the deeply sampled transcriptome data

[17], ultimately produc ing assembly v1.01. Finally, to fur-

ther assess completeness, a scan for the 248 conserved

core genes in the CEGMA database [18] was performed

on all con ifer assemblies (Figure 1B). The resulting an-

notations are classified as full length and partial. The

loblolly pine v1.01 assembly has the largest number of

total annotations (203) of the three conifers as well as

the largest fraction of full length annotations (91%).

For validation purposes, we used a large pool of ap-

proximately 4,600 fosmid clones to approximate a ran-

dom sample of the genome [9]. The sequenced and

assembled pool contained 3,798 contigs longer than

20,000 bp, each putatively representing more than half

of a fosmid insert, with a total span of 109 Mbp. When

aligned to the genome 98.63% of the total length of these

contigs was covered by the WGS assembly. A total of

Neale et al. Genome Biology 2014, 15:R59 Page 2 of 13

http://genomebiology.com/2014/15/3/R59

剩余12页未读，继续阅读

评论收藏

内容反馈

swuhq

粉丝: 0
资源: 1

decoding the massive loblolly pine genome

最新资源

decoding the massive loblolly pine genome

Decoding the World of Quants, Algorithms, and AI.pdf

The Engineer’s Guide to Decoding & Encoding by John Watkinson

Massive Parallel Ldpc Decoding on GPU.pdf

component_decoder.rar_MAAB_The Process_iterative decoding_turbo

Take Assessment: Exercise 1: Decoding Lab English-Analysis

Decoding by linear programming

matlabturbo.zip_lte transmission_turbo Decoding_turbo decoding b

iterative decoding of binary block and convolutional codes

All.About.CAPTCHAs.Decoding.CAPTCHAs.for.Fun

Take Assessment: Exercise 1: Decoding Lab Secret.cpp

sphere decoding

ffmpeg_demuxing_decoding_demo.c例子

警告: Parameters: Character decoding failed. Parameter 'varString' with value '%

ldpc decoding全_LDPC译码_LDPC_

Reed-Solomon Encoding and Decoding.pdf

power_brushlessDCmotor.rar_dc bus control_mosfet inverter_pmsm s

WiMAX.zip_In the Frame_bcjr_turbo_turbo code_wimax turbo

RS ENCODING AND DECODING

manchester coding and decoding

私钥狩猎私钥碰撞工具v1.33

DVB：The Family of International Standards for Digital Video Broadcasting

Iterative Decoding vs Viterbi Decoding A Comarison

Rockable.Decoding.HTML5.2012.RETAIL

Encoding of Certain LDPC Codes with Decoding

zoj 2990 Decoding.md

ADCS_ASS_Q3.rar_The Show_huffman viterbi

最新资源