北美褐藻Saccharina latissima的核和细胞器基因组的支架和注释。

IF 2.8 3区 生物学 Q2 GENETICS & HEREDITY
Frontiers in Genetics Pub Date : 2025-05-14 eCollection Date: 2025-01-01 DOI:10.3389/fgene.2025.1494480
Kelly DeWeese, Gary Molano, Sara Calhoun, Anna Lipzen, Jerry Jenkins, Melissa Williams, Christopher Plott, Jayson Talag, Jane Grimwood, Jean-Luc Jannink, Igor V Grigoriev, Jeremy Schmutz, Charles Yarish, Sergey Nuzhdin, Scott Lindell
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引用次数: 0

摘要

增加新兴水产养殖作物目标的基因组资源可以加快育种进程,正如农业分子育种进展所看到的那样。高质量的带注释参考基因组是实现这种相对较新的分子育种方案所必需的,并且通过提供标准比较工具,有利于群体遗传学、基因发现和基因力学等研究领域。褐藻Saccharina latissima(糖海带)是一种生态和经济上重要的海带,在北太平洋和大西洋都有发现。在北美和欧洲,用于人类消费的甘蔗种植在本世纪显著增加,其单叶形态允许在种植其亚洲姊妹品种Saccharina japonica时采用密集播种的做法。虽然糖藻具有作为人类粮食作物的潜力,但遗传资源信息不足限制了糖海带水产养殖的分子育种。我们从康涅狄格州格罗顿Black Ledge采集的雌性配子体中提取了糖精(Saccharina latisima)的细胞核和细胞器基因组,并进行了支架和注释。该基因组与其他已发表的海带基因组比较,包含218个支架,其中支架N50为1.35 Mb, GC含量为49.84%,预测基因为25,012个。我们还通过比较该糖藻基因组与其他海带基因组的合度和完整性来验证该基因组。我们的团队已经成功地用糖海带进行了最初的基因组选择试验,使用了这个基因组的草图。这个糖藻基因组扩展了经济和生态上重要的糖海带的遗传工具包,将成为未来基础科学、育种和保护工作的基础资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Scaffolded and annotated nuclear and organelle genomes of the North American brown alga Saccharina latissima.

Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica. While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.

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来源期刊
Frontiers in Genetics
Frontiers in Genetics Biochemistry, Genetics and Molecular Biology-Molecular Medicine
CiteScore
5.50
自引率
8.10%
发文量
3491
审稿时长
14 weeks
期刊介绍: Frontiers in Genetics publishes rigorously peer-reviewed research on genes and genomes relating to all the domains of life, from humans to plants to livestock and other model organisms. Led by an outstanding Editorial Board of the world’s leading experts, this multidisciplinary, open-access journal is at the forefront of communicating cutting-edge research to researchers, academics, clinicians, policy makers and the public. The study of inheritance and the impact of the genome on various biological processes is well documented. However, the majority of discoveries are still to come. A new era is seeing major developments in the function and variability of the genome, the use of genetic and genomic tools and the analysis of the genetic basis of various biological phenomena.
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