scholarly journals Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence

2019 ◽  
Vol 9 (11) ◽  
pp. 3513-3520 ◽  
Author(s):  
Ayako Izuno ◽  
Thomas Wicker ◽  
Masaomi Hatakeyama ◽  
Dario Copetti ◽  
Kentaro K. Shimizu
Biotropica ◽  
2018 ◽  
Vol 50 (5) ◽  
pp. 758-767 ◽  
Author(s):  
Pablo Pérez Chaves ◽  
Kalle Ruokolainen ◽  
Hanna Tuomisto

2020 ◽  
Vol 21 (4) ◽  
pp. 301-305
Author(s):  
Kylle Roy ◽  
Kelly A. Jaenecke ◽  
Nikko Bjontegard ◽  
Dan Mikros ◽  
Ellen J. Dunkle ◽  
...  

Rapid ʻōhiʻa death (ROD) is caused by two recently described species of Ceratocystis, C. lukuohia and C. huliohia. These fungi are decimating ʻōhiʻa lehua (Metrosideros polymorpha), the keystone native tree species of Hawaiʻi. Viable Ceratocystis propagules can persist in ambrosia beetle frass (Coleoptera: Scolytinae), and movement of the frass may play a key role in the spread of the disease. In order to prevent the spread of ROD, we developed effective and practical surface (e.g., tools and shoes) decontamination methods to be used by researchers, managers, and the public alike. We first tested different household and laboratory disinfectants on the Ceratocystis fungi in culture, and then we applied the effective culture disinfectants to contaminated ambrosia beetle frass. Laboratory-grade ethanol (70, 80, and 95%), Clorox bleach (10%, 0.825% active ingredient [a.i.]), and isopropanol (70 and 91%), were all equally effective at decontaminating cultured C. lukuohia and C. huliohia. Although all concentrations of isopropanol (50, 70, and 90%) and ethanol (50, 70, and 90%) were effective disinfectants of Ceratocystis-contaminated frass, treatments of frass with up to 20% Clorox bleach (1.2% a.i.) were not completely adequate at killing the fungus. These data reveal that bleach is not a sufficient ROD disinfectant when frass is present, and isopropanol or ethanol are the more reliable options.


2021 ◽  
Vol 118 (37) ◽  
pp. e2023801118
Author(s):  
Jae Young Choi ◽  
Xiaoguang Dai ◽  
Ornob Alam ◽  
Julie Z. Peng ◽  
Priyesh Rughani ◽  
...  

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.


2017 ◽  
Vol 26 (6) ◽  
pp. 1515-1532 ◽  
Author(s):  
Ayako Izuno ◽  
Kanehiro Kitayama ◽  
Yusuke Onoda ◽  
Yuki Tsujii ◽  
Masaomi Hatakeyama ◽  
...  

2000 ◽  
Vol 161 (3) ◽  
pp. 369-379 ◽  
Author(s):  
P. J. Melcher ◽  
S. Cordell ◽  
T. J. Jones ◽  
P. G. Scowcroft ◽  
W. Niemczura ◽  
...  

Author(s):  
Brandon Lind ◽  
Mengmeng Lu ◽  
Dragana Obreht Vidakovic ◽  
Pooja Singh ◽  
Tom Booker ◽  
...  

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Weixue Mu ◽  
Jinpu Wei ◽  
Ting Yang ◽  
Yannan Fan ◽  
Le Cheng ◽  
...  

Nyssa yunnanensis is a deciduous tree species in the family Nyssaceae within the order Cornales. As only eight individual trees and two populations have been recorded in China’s Yunnan province, this species has been listed among China’s national Class I protection species since 1999 and also among 120 PSESP (Plant Species with Extremely Small Populations) in the Implementation Plan of Rescuing and Conserving China’s Plant Species with Extremely Small Populations (PSESP) (2011-2-15). Here, we present the draft genome assembly of N. yunnanensis. Using 10X Genomics linked-reads sequencing data, we carried out the de novo assembly and annotation analysis. The N. yunnanensis genome assembly is 1475 Mb in length, containing 288,519 scaffolds with a scaffold N50 length of 985.59 kb. Within the assembled genome, 799.51 Mb was identified as repetitive elements, accounting for 54.24% of the sequenced genome, and a total of 39,803 protein-coding genes were predicted. With the genomic characteristics of N. yunnanensis available, our study might facilitate future conservation biology studies to help protect this extremely threatened tree species.


Author(s):  
Jiaoyu He ◽  
Shanfei bao ◽  
Junhang Deng ◽  
Qiufu Li ◽  
zhilin song ◽  
...  

The A.nanchuanensis (Artocarpus Nanchuanensis, Moraceae) is an evergreen Artocarpus genus representative tree species in the northernmost natural distribution and one of the extremely endangered tree species in China. In this study, we obtained a high-quality chromosome-scale genome assembly and annotation for A.nanchuanensis using inter-grated approaches, including Illumina, Nanopore sequencing platform as well as Hi-C. A total of 128.71 gigabases (Gb) raw Nanopore Sequel reads were generated from 20 kb libraries. After filtering, 123.38 Gb clean reads were obtained, giving 160.34x coverage depth. The final assembled A.nanchuanensis genome was 769.44 Mb with a contig N50 of 2.09 Mb, and 99.62% (766.50 Mb) of the assembly data was assigned to 28 pseudochromosomes. Gene modelling predicted 41,636 protein-coding genes, of which 95.10% were annotated. The gene annotation completeness was evaluated by BUSCO, and 94.44% conserved genes could be found in the assembly data. The disclosure of A.nanchuanensis genome sequence information provides an important resource to expand our understanding of the molecular mechanism in its unique biological processes and nutritional, medicinal benefits.


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