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评估巨基因组的基因组成：糖松（兰伯氏松）

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

作者信息

Gonzalez-Ibeas Daniel, Martinez-Garcia Pedro J, Famula Randi A, Delfino-Mix Annette, Stevens Kristian A, Loopstra Carol A, Langley Charles H, Neale David B, Wegrzyn Jill L

机构信息

Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269.

Department of Plant Sciences, University of California, Davis, California 95616.

出版信息

G3 (Bethesda). 2016 Dec 7;6(12):3787-3802. doi: 10.1534/g3.116.032805.

DOI:10.1534/g3.116.032805
PMID:27799338
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5144951/
Abstract

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.

摘要

糖松（Pinus lambertiana Douglas）属于Strobus亚属，估计基因组大小为31 Gbp。由于针叶树的巨大基因组在基因识别方面存在挑战，转录组资源对针叶树尤为重要。在本研究中，我们通过对多种组织类型进行深度测序，首次对糖松转录组进行了全面调查，生成了超过25亿条短读段。针叶树中首次纳入了通过PacBio Iso-Seq生成的第三代长读段，以应对与从头转录组组装相关的挑战。本文提供了一项技术比较，有助于弥补植物物种中第二代和第三代转录组测序方法比较稀缺的情况。此外，转录组参考对于负责整个基因组测序和组装的平行项目中的基因模型识别和质量评估至关重要。在本研究中，转录组数据还用于解决针叶树中与谱系特异性Dicer样蛋白相关的问题。这些蛋白在针叶树中可转座元件增殖控制和相关基因组扩展中发挥作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/72d1cd5742cd/3787f8.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/9705c960e181/3787f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/2fa3efc0903f/3787f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/23411ca5ef9d/3787f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/72d1cd5742cd/3787f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/e49ab445f05f/3787f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/43c2e5952a41/3787f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/dbd604cf0303/3787f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/9705c960e181/3787f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/2fa3efc0903f/3787f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/23411ca5ef9d/3787f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a33a/5144951/72d1cd5742cd/3787f8.jpg

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