Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants

Minhui Shi; Fei Chen; Sunil Kumar Sahu; Qing Wang; Shangchen Yang; Zhihong Wang; Jin Chen; Huan Liu; Zhijun Hou; Sheng-Guo Fang; Tianming Lan

doi:10.1038/s41597-023-02729-4

Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants

Sci Data. 2024 Jan 11;11(1):63. doi: 10.1038/s41597-023-02729-4.

Authors

Minhui Shi^#^{1

2

3}, Fei Chen^#^{4

5}, Sunil Kumar Sahu^#², Qing Wang², Shangchen Yang⁶, Zhihong Wang^{4

5}, Jin Chen^{7

8}, Huan Liu^{1

2

7}, Zhijun Hou⁹, Sheng-Guo Fang¹⁰, Tianming Lan^{11

12

13}

Affiliations

¹ BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
² State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
³ College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming, 650031, China.
⁵ Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming, 650031, China.
⁶ MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
⁷ Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
⁸ China National GeneBank, BGI Research, Shenzhen, 518083, China.
⁹ College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.
¹⁰ MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. sgfanglab@zju.edu.cn.
¹¹ BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China. lantianming@genomics.cn.
¹² State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China. lantianming@genomics.cn.
¹³ College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China. lantianming@genomics.cn.

^# Contributed equally.

Abstract

The Proboscidea, which includes modern elephants, were once the largest terrestrial animals among extant species. They suffered mass extinction during the Ice Age. As a unique branch on the evolutionary tree, the Proboscidea are of great significance for the study of living animals. In this study, we generate chromosome-scale and haplotype-resolved genome assemblies for two extant Proboscidea species (Asian Elephant, Elephas maximus and African Savannah Elephant, Loxodonta africana) using Pacbio, Hi-C, and DNBSEQ technologies. The assembled genome sizes of the Asian and African Savannah Elephant are 3.38 Gb and 3.31 Gb, with scaffold N50 values of 130 Mb and 122 Mb, respectively. Using Hi-C technology ~97% of the scaffolds are anchored to 29 pseudochromosomes. Additionally, we identify ~9 Mb Y-linked sequences for each species. The high-quality genome assemblies in this study provide a valuable resource for future research on ecology, evolution, biology and conservation of Proboscidea species.

Publication types

Dataset

MeSH terms

Animals
Chromosomes / genetics
Elephants* / genetics
Genome*
Haplotypes