Erratum: The sequence and de novo assembly of the giant panda genome

Li, Ruiqiang; Fan, Wei; Tian, Geng; Zhu, Hongmei; He, Lin; Cai, Jing; Huang, Quanfei; Cai, Qingle; Li, Bo; Bai, Yinqi; Zhang, Zhihe; Zhang, Yaping; Wang, Wen; Li, Jun; Wei, Fuwen; Li, Heng; Jian, Min; Li, Jianwen; Zhang, Zhaolei; Nielsen, Rasmus; Li, Dawei; Gu, Wanjun; Yang, Ze‐Peng; Xuan, Zhaoling; Ryder, Oliver A.; Leung, Frederick Chi-Ching; Zhou, Yan; Cao, Jianjun; Sun, Xiao; Fu, Yonggui; Fang, Xiaodong; Guo, Xiaosen; Wang, Bo; Hou, Rong; Shen, Fang; Mu, Bo; Ni, Peixiang; Lin, Runmao; Qian, Wubin; Wang, Guodong; Yu, Chang; Nie, Wei; Wang, Jinhuan; Wu, Zhigang; Liang, Huiqing; Jiang, Min; Wu, Qi; Cheng, Shifeng; Ruan, Jue; Wang, Mingwei; Shi, Zhang; Wen, Ming; Liu, Binghang; Ren, Xiaoli; Zheng, Huisong; Dong, Dong; Cook, Kathleen; Gao, Shan; Zhang, Hao; Kosiol, Carolin; Xie, Xueying; Zhang, Lu; Zheng, Hancheng; Li, Yingrui; Steiner, Cynthia C.; Lam, Tommy Tsan-Yuk; Lin, Siyuan; Zhang, Qinghui; Li, Guoqing; Tian, Jing; Gong, Timing; Liu, Hongde; Zhang, Dejin; Fang, Lin; Wang, Hongzhi; Zhang, Juanbin; Hu, Wenbo; Xu, Anlong; Ren, Yuanyuan; Zhang, Guojie; Bruford, Michael William; Li, Qibin; Ma, Lijia; Guo, Yiran; An, Na; Hu, Yujie; Zheng, Yusheng; Shi, Yongyong; Li, Zhiqiang; Liu, Qing; Chen, Yanling; Zhao, Jing; Qu, Ning; Zhao, Shancen; Tian, Feng; Wang, Xiaoling; Wang, Haiyin; Xu, Lizhi; Liu, Xiao; Vinař, Tomáš; Wang, Yajun; Lam, Tak-Wah; Yiu, Siu-Ming; Liu, Shiping; Zhang, Hemin; Li, Desheng; Huang, Yan; Wang, Xia; Yang, Guohua; Jiang, Zhi; Wang, Junyi; Qin, Nan; Li, Li; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Wong, Gane Ka‐Shu; Olson, Maynard V.; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

doi:10.1038/nature08846

Cited by 10 publications

(4 citation statements)

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“…The distribution of k-mer frequencies was estimated with jellyfish [37] using 100 bp reads from the 300 bp insert-size library. K-mer statistics were used to estimate the genome size and varied from 650 to 700 Mbp depending on the value of k (Additional file 2: Figure S3) [38, 39]. The number of scaffolds greater than 1000 bp in size was 14000 and the scaffold N50 was 85000.…”

Section: Resultsmentioning

confidence: 99%

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

et al. 2014

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BackgroundTef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef’s desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource.ResultsThe draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten.ConclusionsIt is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-581) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

et al. 2014

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“…Therefore, bamboo DNA sequences were filtered before analysing the data. bowtie2 (Langmead et al, 2009), samtools (Li et al, 2009) and bam2fastq (https://gsl.hudso nalpha.org/infor matio n/softw are/ bam2f astq) were employed to remove host and bamboo sequences (sequences with at least 90% similarity to the reference giant panda and (Li et al, 2010) bamboo (Peng et al, 2013) genome). Quality control was performed using a sliding window (5-bp bases) by trimmomatic software (Bolger et al, 2014) using the following criteria: (i) cutting was performed when the average quality within the window fell below Q 20; (ii) clean reads did not contain any N-base; (iii) trimming was applied to the 3′ end of reads, and reads below 125 bp length were dropped; and (iv) only paired-end reads were retained for downstream analyses.…”

Section: Metagenome Analysismentioning

confidence: 99%

“…Although the panda is herbivorous in diet, it possesses a typical carnivore digestive system with a short and simple gastrointestinal tract (Quay & Davis, 1966). The panda genome encodes all necessary mammalian enzymes but lacks cellulosedegrading genes (Li et al, 2010). The gut microbiome plays a crucial role in extracting nutrients from high-fibre bamboo by digesting cellulose (Zhu et al, 2011), hemicellulose (Zhang et al, 2018) and lignin (Fang et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Microbial species from multiple maternal body sites shape the developing giant panda (Ailuropoda melanoleuca) cub gut microbiome

et al. 2023

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The gut microbiome of the giant panda (Ailuropoda melanoleuca) plays a vital role in nutrient acquisition from its specialized bamboo diet. Giant panda cubs harbour significantly different gut microbiota during their growth and development when feeding on milk before switching to bamboo. The fetal gut is sterile, and following birth, mother-to-infant microbial transmission has been implicated as a seeding source for the infant gut microbiota. Details of this transmission in giant pandas remain unclear.

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“…Whole genome SNV rates for solenodon were calculated, defined as a ratio of all observed SNVs to all possible SNV sites in the genome were found to be comparatively low among other mammals (Figure 8) [76][77][78][79]. To enable this comparison, the same calculations were employed,…”

Section: Genomic Variation and Demographic History Inferencementioning

confidence: 99%

Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangeredSolenodon paradoxusfrom the island of Hispaniola

Grigorev

Kliver

Dobrynin

et al. 2017

Preprint

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Solenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly for solenodons has never been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation has likely resulted in extreme homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies for performance with genetically impoverished species' genomes. The string-graph based assembly strategy seems a better choice compared to the conventional de Brujn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (S. p. woodi). In addition, we obtained one additional sequence of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on the venomous genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. Patterns of SNP variation allowed us to infer population demography, which indicated a subspecies split within the Hispaniolan solenodon at least 300 Kya.

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Erratum: The sequence and de novo assembly of the giant panda genome

Abstract: In this Article, the Latin species name of the giant panda was written incorrectly as Ailuropoda melanoleura. The correct name is Ailuropoda melanoleuca.

Cited by 10 publications

References 1 publication

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

Microbial species from multiple maternal body sites shape the developing giant panda (Ailuropoda melanoleuca) cub gut microbiome

Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangeredSolenodon paradoxusfrom the island of Hispaniola

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